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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
...of neighboring sequences corresponding to KRAB and C2H2 poly-zinc finger domains, 378 of which were predicted to encode full-length KZFPs. We could also delineate 31 clusters, that is, groups of at least three genes separated by <250 kb as previously defined (Huntley et al. 2006) (Fig. 1A; Supplemental Table S1...
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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: Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
- Metewo Selase Enuameh,
- Yuna Asriyan,
- Adam Richards,
- Ryan G. Christensen,
- Victoria L. Hall,
- Majid Kazemian,
- Cong Zhu,
- Hannah Pham,
- Qiong Cheng,
- Charles Blatti,
- Jessie A. Brasefield,
- Matthew D. Basciotta,
- Jianhong Ou,
- Joseph C. McNulty,
- Lihua J. Zhu,
- Susan E. Celniker,
- Saurabh Sinha,
- Gary D. Stormo,
- Michael H. Brodsky,
- and Scot A. Wolfe
Genome Res. June 2013 23: 928-940; Published in Advance March 7, 2013, doi:10.1101/gr.151472.112
...Global analysis of Drosophila Cys 2 -His 2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants Metewo Selase Enuameh 1 , Yuna Asriyan 1 , Adam Richards 1 , Ryan G. Christensen 2 , Victoria L. Hall 1...
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Method: Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
- Shaleen Shrestha,
- Jared Allan Sewell,
- Clarissa Stephanie Santoso,
- Elena Forchielli,
- Sebastian Carrasco Pro,
- Melissa Martinez,
- and Juan Ignacio Fuxman Bass
Genome Res. September 2019 29: 1533-1544; doi:10.1101/gr.248823.119
...are ordered by family. (B) Distribution by family for TFs that interact with at least 20% of the Alu sequences tested, compared to the distribution of TFs in the eY1H array. (NHR) nuclear hormone receptor, (ZF-DHHC) zinc finger DHHC, (ZF-C2H2) zinc finger Cys2His2, (HD) homeodomain, (ETS) E26 transformation...
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Method: Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
- Yiming Kang,
- Nikhil R. Patel,
- Christian Shively,
- Pamela Samantha Recio,
- Xuhua Chen,
- Bernd J. Wranik,
- Griffin Kim,
- R. Scott McIsaac,
- Robi Mitra,
- and Michael R. Brent
Genome Res. March 2020 30: 459-471; Published in Advance February 14, 2020, doi:10.1101/gr.259655.119
...: ChIP-TF_over = 80). Asterisk indicates that no fixed threshold analysis for HEK293 is available due to the lack of response P-values.We also analyzed a data set on 88 human GFP-tagged C2H2 zinc finger TFs with matched ChIP-seq data and response-to-overexpression data in HEK293 cells (Schmitges et al...
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Method: Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants
- Dongwon Lee,
- Ashish Kapoor,
- Alexias Safi,
- Lingyun Song,
- Marc K. Halushka,
- Gregory E. Crawford,
- and Aravinda Chakravarti
Genome Res. October 2018 28: 1577-1588; Published in Advance August 23, 2018, doi:10.1101/gr.234633.118
...matrices (PWMs) of C2H2 Zinc-Finger (ZF) TFs (Schmitges et al. 2016), to show that 11-mers matching 54% of PWMs (473/868) associated with 506 TFs were enriched in the top fifth percentile of the distribution (Supplemental Data S1). As expected, 11-mers matching these predicted cardiac TFs systematically...
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Research: The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes
- Luisa Robbez-Masson,
- Christopher H.C. Tie,
- Lucia Conde,
- Hale Tunbak,
- Connor Husovsky,
- Iva A. Tchasovnikarova,
- Richard T. Timms,
- Javier Herrero,
- Paul J. Lehner,
- and Helen M. Rowe
Genome Res. May 4, 2018 ; Published in Advance May 4, 2018, doi:10.1101/gr.228171.117
...M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, et al. 2016. Multiparameter functional diversity of human C2H2 zinc finger proteins. Genome Res 26: 1742–1752. Sookdeo A, Hepp CM, McClure MA, Boissinot S. 2013. Revisiting the evolution of mouse LINE-1 in the genomic era. Mob DNA 4...
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