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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
...no significant sequence similarity to known protein domains but is highly conserved across cyprinid ZNFs and is enriched in negatively charged glutamic acid residues, a feature it shares with the KRAB domain (Bonferroni-corrected P-value < 0.00125 for both, relative to sequences in the SwissProt51 database...
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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
..., and ZNF117) near the centromere (Fig. 1A; Supplemental Fig. S1).View larger version: In this window In a new window Figure 1. Human KRAB-zinc finger proteins (KZFPs) and their evolution in the primate lineage. (A) Dots indicate relative chromosomal position of KZFP genes (defined by juxtaposed KRAB...
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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
...types of bait and prey proteins. See also Supplemental Figures S3–S5, Supplemental Tables S5–S9. Functional diversity of human C2H2-ZF proteins Genome Research 1747 www..org C2H2-ZF proteins with well-characterized effector domains. KRAB-containing C2H2-ZF proteins typically associate with TRIM28 (38...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
....Cytosine methylation plays a critical role in genomic imprinting, gene regulation, X-Chromosome inactivation (XCI), cellular differentiation, aging, and tumorigenesis. Cells have an extensive system of proteins that establish these methylation patterns through de novo methylation or demethylation, copy methylation...
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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
...different preferences. Transposable elements are a source of genetic novelty between populations and species, driving rapid adaptive evolution. However, the extent of TEs’ contribution to host shift remains unexplored. Here, we perform genomic and transcriptomic analyses in six s of cactophilic species...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...eliminate tens of thousands of DNA sequences from a germline copy. Recently, we showed that the chromatin remodeler ISWI1 is required for somatic development in the ciliate Paramecium tetraurelia. Here, we describe two high similarity paralogous proteins, ICOPa and ICOPb, essential for their editing. ICOPa...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...pressures on TEs with distinct regulatory roles.Genome evolution through TE activity is also likely influenced by WGDs. Because WGDs result in cellular stress, TEs can escape host-silencing mechanisms following WGDs. This is supported by both experimental (Kashkush et al. 2002, 2003; Kraitshtein et al. 2010...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...six different genomic deletions spanning RE1–3 (Supplemental Fig. S48B) or sgRNAs for mCherry or EGFP as controls. The Cas9 protein was equally expressed from all vectors in C1 cells compared with GAPDH (Supplemental Fig. S48C). After 2 days of puromycin selection for Cas9-expressing C1 cells, we...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...of genomic and transcriptomic convergence.Here we studied the effects of timescale on repeated genomic and transcriptomic evolution associated with transition to arid environments (Fig. 1A). First, we quantified signals of repeated evolution at two timescales, corresponding to the order Rodentia...
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