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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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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
.... Predicted 5′ ends on many (but not all) of the genes in the cluster overlap with the same type of LTR repeat sequence, which may indicate that the repeats are involved in driving gene expression, as has been shown previously for other genes including related zinc finger genes ( Di Cristofano et al. 1995...
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RESOURCE: A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors
- Stuart Huntley,
- Daniel M. Baggott,
- Aaron T. Hamilton,
- Mary Tran-Gyamfi,
- Shan Yang,
- Joomyeong Kim,
- Laurie Gordon,
- Elbert Branscomb,
- and Lisa Stubbs
Genome Res. May 2006 16: 669-677; Published in Advance April 10, 2006, doi:10.1101/gr.4842106
...domains. Mol. Cell. Biol. 21 : 3609 – 3615 . ↵ Eichler E.E. , Hoffman S.M. , Adamson A.A. , Gordon L.A. , McCready P. , Lamerdin J.E. , Mohrenweiser H.W. ( 1998 ) Complex β-satellite repeat structures and the expansion of the zinc finger gene cluster in 19p12. Genome Res. 8 : 791 – 808 . ↵ Eisen M...
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Article: Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing
- Jung-Hyun Kim,
- Thomas Ebersole,
- Natalay Kouprina,
- Vladimir N. Noskov,
- Jun-Ichirou Ohzeki,
- Hiroshi Masumoto,
- Brankica Mravinac,
- Beth A. Sullivan,
- Adam Pavlicek,
- Sinisa Dovat,
- Svetlana D. Pack,
- Yoo-Wook Kwon,
- Patrick T. Flanagan,
- Dmitri Loukinov,
- Victor Lobanenkov,
- and Vladimir Larionov
Genome Res. April 2009 19: 533-544; Published in Advance January 13, 2009, doi:10.1101/gr.086496.108
...expression during cellular differentiation or reprogramming. For example, development of mouse hematopoietic cells is regulated by zinc finger proteins encoded by the Ikaros gene (ikzf1) (for review, see Ng et al. 2007) that bind to pericentromeric heterochromatin as well as to regulatory sequences...
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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...-specifically methylated regions (Irizarry et al. 2009), these genes are significantly enriched in embryonic development, including the highly divergent homeobox gene HDX along with several neuronal growth factors NEGR1, NETO1, and NTM. In addition, we observe significant enrichment for zinc finger genes, Kruppel...
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Research: A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation
- Hala Al Adhami,
- Brendan Evano,
- Anne Le Digarcher,
- Charlotte Gueydan,
- Emeric Dubois,
- Hugues Parrinello,
- Christelle Dantec,
- Tristan Bouschet,
- Annie Varrault,
- and Laurent Journot
Genome Res. March 2015 25: 353-367; Published in Advance January 22, 2015, doi:10.1101/gr.175919.114
...A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation Hala Al Adhami 1 , 2 , 3 , 4 , 6 , Brendan Evano 1 , 2 , 3 , 4 , 7...
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ARTICLE: Complex genomic rearrangements lead to novel primate gene function
- Francesca D. Ciccarelli,
- Christian von Mering,
- Mikita Suyama,
- Eoghan D. Harrington,
- Elisa Izaurralde,
- and Peer Bork
Genome Res. March 2005 15: 343-351; Published in Advance February 14, 2005, doi:10.1101/gr.3266405
...is followed by RanGTP-binding domains (RanBP1 homologous domains or RBD) related to the one present in RanBP1, a variable number of zinc-finger motifs, and a C terminus with homology to cyclophilin A ( Fig. 1A ). View larger version: In this window In a new window Figure 1. Conservation of the RanBP2 gene...
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LETTER: Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
- Ann-Marie Mallon,
- Laurens Wilming,
- Joseph Weekes,
- James G.R. Gilbert,
- Jennifer Ashurst,
- Sandrine Peyrefitte,
- Lucy Matthews,
- Matthew Cadman,
- Richard McKeone,
- Chris A. Sellick,
- Ruth Arkell,
- Marc R.M. Botcherby,
- Mark A. Strivens,
- R. Duncan Campbell,
- Simon Gregory,
- Paul Denny,
- John M. Hancock,
- Jane Rogers,
- and Steve D.M. Brown
Genome Res. October 2004 14: 1888-1901; Published in Advance September 13, 2004, doi:10.1101/gr.2478604
..., and segments 4 and 8 showed nine- to 10-fold excesses. ECRs and Gene Identification A subsequent analysis of mouse-human ECRs allowed us to identify additional and variant exons. We also identified a novel SCAN domain containing C2H2 type zinc-finger protein (933017L02Rik) that was missed in the original...
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LETTER: An ORFeome-based Analysis of Human Transcription Factor Genes and the Construction of a Microarray to Interrogate Their Expression
- David N. Messina,
- Jarret Glasscock,
- Warren Gish,
- and Michael Lovett
Genome Res. October 15, 2004 14: 2041-2047; doi:10.1101/gr.2584104
....M., Adamson, A.A., Gordon, L.A., McCready, P., Lamerdin, J.E., and Mohrenweiser, H.W. 1998 . Complex β-satellite repeat structures and the expansion of the zinc finger gene cluster in 19p12. Genome Res. 8 : 791 -808. ↵ Enard, W., Przeworski, M., Fisher, S.E., Lai, C.S.L., Wiebe, V., Kitano, T., Monaco, A...

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