Characterization and design of C2H2 zinc finger proteins as custom DNA binding domains

2008 ◽  
Author(s):  
Jeffry D. Sander
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Finger Proteins ◽  
C2h2 Zinc Finger ◽  
Dna Binding Domains ◽  
Binding Domains

scholarly journals Artificial Zinc Finger DNA Binding Domains: Versatile Tools for Genome Engineering and Modulation of Gene Expression

2015 ◽  
Vol 116 (11) ◽  
pp. 2435-2444 ◽  
Author(s):  
Mir A. Hossain ◽  
Joeva J. Barrow ◽  
Yong Shen ◽  
MD Imdadul Haq ◽  
Jörg Bungert
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Zinc Finger ◽  
Genome Engineering ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Modulation Of Gene Expression

scholarly journals The Role of Zinc Finger Linkers in Zinc Finger Protein Binding to DNA

2020 ◽  
Author(s):  
Mazen Hamed ◽  
Reema Siam ◽  
Roza Zaid
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Md Simulations ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Finger Protein ◽  
The Right

Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.

scholarly journals Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters

2020 ◽  
Vol 48 (11) ◽  
pp. 5986-6000 ◽  
Author(s):  
Weiya Ni ◽  
Andrew A Perez ◽  
Shannon Schreiner ◽  
Charles M Nicolet ◽  
Peggy J Farnham
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Cpg Island ◽  
Zinc Finger Proteins ◽  
Double Knockout ◽  
Altered Expression ◽  
C2h2 Zinc Finger ◽  
Necessary And Sufficient ◽  
Functional Analyses

Abstract Our study focuses on a family of ubiquitously expressed human C2H2 zinc finger proteins comprised of ZFX, ZFY and ZNF711. Although their protein structure suggests that ZFX, ZFY and ZNF711 are transcriptional regulators, the mechanisms by which they influence transcription have not yet been elucidated. We used CRISPR-mediated deletion to create bi-allelic knockouts of ZFX and/or ZNF711 in female HEK293T cells (which naturally lack ZFY). We found that loss of either ZFX or ZNF711 reduced cell growth and that the double knockout cells have major defects in proliferation. RNA-seq analysis revealed that thousands of genes showed altered expression in the double knockout clones, suggesting that these TFs are critical regulators of the transcriptome. To gain insight into how these TFs regulate transcription, we created mutant ZFX proteins and analyzed them for DNA binding and transactivation capability. We found that zinc fingers 11–13 are necessary and sufficient for DNA binding and, in combination with the N terminal region, constitute a functional transactivator. Our functional analyses of the ZFX family provides important new insights into transcriptional regulation in human cells by members of the large, but under-studied family of C2H2 zinc finger proteins.

Base sequence discrimination by zinc-finger DNA-binding domains

Nature ◽  
1991 ◽  
Vol 349 (6305) ◽  
pp. 175-178 ◽  
Author(s):  
Jeannette Nardelli ◽  
Toby J. Gibson ◽  
Christine Vesque ◽  
Patrick Charnay
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Base Sequence ◽  
Dna Binding Domains ◽  
Binding Domains

scholarly journals Male-specific Fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 659 ◽  
Author(s):  
Justin E Dalton ◽  
Justin M Fear ◽  
Simon Knott ◽  
Bruce S Baker ◽  
Lauren M McIntyre ◽  
...  
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Male Specific

Developmentally Regulated Mouse Gene NK10 Encodes a Zinc Finger Repressor Protein with Differential DNA-Binding Domains

1995 ◽  
Vol 14 (11) ◽  
pp. 971-981 ◽  
Author(s):  
RITA LANGE ◽  
ANNETTE CHRISTOPH ◽  
HANS-JÜRGEN THIESEN ◽  
GABY VOPPER ◽  
KENNETH R. JOHNSON ◽  
...  
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Mouse Gene ◽  
Developmentally Regulated ◽  
Repressor Protein ◽  
Dna Binding Domains ◽  
Binding Domains

scholarly journals Characterization of the DNA-binding properties of the myeloid zinc finger protein MZF1: two independent DNA-binding domains recognize two DNA consensus sequences with a common G-rich core.

1994 ◽  
Vol 14 (3) ◽  
pp. 1786-1795 ◽  
Author(s):  
J F Morris ◽  
R Hromas ◽  
F J Rauscher
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Zinc Finger ◽  
Binding Sites ◽  
Zinc Fingers ◽  
Consensus Sequences ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Gel Shift ◽  
Myeloid Zinc Finger

The myeloid zinc finger gene 1, MZF1, encodes a transcription factor which is expressed in hematopoietic progenitor cells that are committed to myeloid lineage differentiation. MZF1 contains 13 C2H2 zinc fingers arranged in two domains which are separated by a short glycine- and proline-rich sequence. The first domain consists of zinc fingers 1 to 4, and the second domain is formed by zinc fingers 5 to 13. We have determined that both sets of zinc finger domains bind DNA. Purified, recombinant MZF1 proteins containing either the first set of zinc fingers or the second set were prepared and used to affinity select DNA sequences from a library of degenerate oligonucleotides by using successive rounds of gel shift followed by PCR amplification. Surprisingly, both DNA-binding domains of MZF1 selected similar DNA-binding consensus sequences containing a core of four or five guanine residues, reminiscent of an NF-kappa B half-site: 1-4, 5'-AGTGGGGA-3'; 5-13, 5'-CGGGnGAGGGGGAA-3'. The full-length MZF1 protein containing both sets of zinc finger DNA-binding domains recognizes synthetic oligonucleotides containing either the 1-4 or 5-13 consensus binding sites in gel shift assays. Thus, we have identified the core DNA consensus binding sites for each of the two DNA-binding domains of a myeloid-specific zinc finger transcription factor. Identification of these DNA-binding sites will allow us to identify target genes regulated by MZF1 and to assess the role of MZF1 as a transcriptional regulator of hematopoiesis.

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