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SysZNF: the C2H2 zinc finger gene database

G. Ding, P. Lorenz, M. Kreutzer, Y. Li, H.-J. Thiesen
2009 Nucleic Acids Research  
C2H2 zinc finger (C2H2-ZNF) genes are one of the largest and most complex gene super-families in metazoan genomes, with hundreds of members in the human and mouse genome.  ...  Here, we systematically collected all the C2H2-ZNF genes in the human and mouse genome and constructed a database named SysZNF to deposit available datasets related to these genes.  ...  Defined C2H2-ZNF motifs have been applied to engineer custom zinc-finger nucleases (ZFN) for gene therapy (11) .  ... 
doi:10.1093/nar/gkn782 pmid:18974185 pmcid:PMC2686507 fatcat:bvqjurl6nffbniz2krep4wmdeu

A study on the distribution of 37 well conserved families of C2H2 zinc finger genes in eukaryotes

Arun Seetharam, Gary W Stuart
2013 BMC Genomics  
The C2H2 zinc-finger (ZNF) containing gene family is one of the largest and most complex gene families in metazoan genomes.  ...  We succeeded in identifying 3,890 genes as distinct members of 37 C2H2 gene families.  ...  Some of the sequence data used in this study were produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with the user community.  ... 
doi:10.1186/1471-2164-14-420 pmid:23800006 pmcid:PMC3701560 fatcat:zpwvvwhprngazoh6fvmtiirhtq

A common mode of recognition for methylated CpG

Yiwei Liu, Xing Zhang, Robert M. Blumenthal, Xiaodong Cheng
2013 TIBS -Trends in Biochemical Sciences. Regular ed  
Two recent structures of C2H2 zinc finger (ZnF) proteins in complex with methylated DNA reveal a common recognition mode for 5-methylcytosine (5mC) that involves a 5mC-Arg-G triad.  ...  We propose that the RH-ZnF motifs provide specificity for 5mCpG, whereas the neighboring Zn fingers recognize the surrounding DNA sequence context.  ...  The C2H2 Zinc Finger Gene database (SysZNF) was searched for ZnFs containing RH motifs at the proper position [39] .  ... 
doi:10.1016/j.tibs.2012.12.005 pmid:23352388 pmcid:PMC3608759 fatcat:fmm2u52wwrfndp5bcqxsl2vkcm

Re-programming DNA-binding specificity in zinc finger proteins for targeting unique address in a genome

Abhinav Grover, Akshay Pande, Krishna Choudhary, Kriti Gupta, Durai Sundar
2010 Journal of Systems and Synthetic Biology  
Here, we explore the novel functionality obtained by engineered zinc finger proteins and the computational approaches for prediction of recognition helices of zinc finger proteins that can raise our ability  ...  Custom-design of zinc finger proteins with tailor-made specificity is currently limited by the availability of information on recognition helices for all possible DNA targets.  ...  the IYBA scheme.  ... 
doi:10.1007/s11693-011-9077-4 pmid:22132059 pmcid:PMC3065587 fatcat:ldcs67bzvrbtnokf7w7kxf32im

The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues

Peter Lorenz, Sabine Dietmann, Thomas Wilhelm, Dirk Koczan, Sandra Autran, Sophie Gad, Gaiping Wen, Guohui Ding, Yixue Li, Marie-Françoise Rousseau-Merck, Hans-Juergen Thiesen
2010 BMC Genomics  
Expansion of multi-C2H2 domain zinc finger (ZNF) genes, including the Krüppel-associated box (KRAB) subfamily, paralleled the evolution of tetrapodes, particularly in mammalian lineages.  ...  The analysis of orthologs in therian mammalian species revealed strong conservation and purifying selection of the KRAB-A and zinc finger domains.  ...  We are grateful to all colleagues that provided the scientific community with freely available software tools and databases.  ... 
doi:10.1186/1471-2164-11-206 pmid:20346131 pmcid:PMC2865497 fatcat:52vvpmdenffmxpxvcpbd7skgui

A New Family of Predicted Krüppel-Like Factor Genes and Pseudogenes in Placental Mammals

Jimin Pei, Nick V. Grishin, Eugene Yujun Xu
2013 PLoS ONE  
Predicted KLF18 proteins maintain conserved features in the zinc fingers of the SP/KLF family, while possessing repeats of a unique sequence motif in their N-terminal regions.  ...  Krüppel-like factors (KLF) and specificity proteins (SP) constitute a family of zinc-finger-containing transcription factors that play important roles in a wide range of processes including differentiation  ...  Acknowledgements We would like to thank Lisa Kinch for critical reading of the manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0081109 pmid:24244731 pmcid:PMC3820594 fatcat:3hxk4ycx3jenvngrfrykdzpnhy

DNA Recognition of 5-Carboxylcytosine by a Zfp57 Mutant at an Atomic Resolution of 0.97 Å

Yiwei Liu, Yusuf Olatunde Olanrewaju, Xing Zhang, Xiaodong Cheng
2013 Biochemistry  
The Zfp57 gene encodes a KRAB (Krüppel-associated box) domain-containing C2H2 zinc finger transcription factor that is expressed in early development.  ...  In the previously determined structure of the mouse Zfp57 DNA-binding domain in complex with DNA containing 5-methylcytosine (5mC), the side chains of Arg178 and Glu182 contact the methyl group via hydrophobic  ...  Eric Ortlund for comments on the manuscript. X-ray data were collected at Southeast Regional Collaborative Access Team (SER-CAT) 22-ID beamline at the Advanced Photon Source. The  ... 
doi:10.1021/bi401360n pmid:24236546 pmcid:PMC3884566 fatcat:zwutszcskbd4dkeajff47hamqq

Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins [chapter]

A. Patel, H. Hashimoto, X. Zhang, X. Cheng
2016 Methods in Enzymology  
Among the known methylated DNA-binding domains, the Cys2-His2 zinc finger (ZnF) protein superfamily is the largest with hundreds of members, each containing tandem ZnFs ranging from 3 to >30 fingers.  ...  This work was supported by grant from the National Institutes of Health GM049245-22 to X.C. (who is a Georgia Research Alliance Eminent Scholar).  ...  The SysZNF database was examined for Krüppel-associated box (KRAB)-ZnF proteins in human (A) or mouse (B).  ... 
doi:10.1016/bs.mie.2016.01.019 pmid:27372763 pmcid:PMC4941819 fatcat:h62xlulxpvelxm2lu5bz2s4uja