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

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.

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Base sequence discrimination by zinc-finger DNA-binding domains

Nature ◽

10.1038/349175a0 ◽

1991 ◽

Vol 349 (6305) ◽

pp. 175-178 ◽

Cited By ~ 136

Author(s):

Jeannette Nardelli ◽

Toby J. Gibson ◽

Christine Vesque ◽

Patrick Charnay

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Base Sequence ◽

Dna Binding Domains ◽

Binding Domains

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

BMC Genomics ◽

10.1186/1471-2164-14-659 ◽

2013 ◽

Vol 14 (1) ◽

pp. 659 ◽

Cited By ~ 39

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

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BSAP Can Repress Enhancer Activity by Targeting PU.1 Function

Molecular and Cellular Biology ◽

10.1128/mcb.20.6.1911-1922.2000 ◽

2000 ◽

Vol 20 (6) ◽

pp. 1911-1922 ◽

Cited By ~ 53

Author(s):

Shanak Maitra ◽

Michael Atchison

Keyword(s):

Transcription Factors ◽

Cell Differentiation ◽

Dna Binding ◽

B Cell ◽

Transactivation Domain ◽

B Cell Differentiation ◽

Developmentally Regulated ◽

Enhancer Activity ◽

Dna Binding Domains ◽

Binding Domains

ABSTRACT PU.1 and BSAP are transcription factors crucial for proper B-cell development. Absence of PU.1 results in loss of B, T, and myeloid cells, while absence of BSAP results in an early block in B-cell differentiation. Both of these proteins bind to the immunoglobulin κ chain 3′ enhancer, which is developmentally regulated during B-cell differentiation. We find here that BSAP can repress 3′ enhancer activity. This repression can occur in plasmacytoma lines or in a non-B-cell line in which the enhancer is activated by addition of the appropriate enhancer binding transcription factors. We show that the transcription factor PU.1 is a target of the BSAP-mediated repression. Although PU.1 and BSAP can physically interact through their respective DNA binding domains, this interaction does not affect DNA binding. When PU.1 function is assayed in isolation on a multimerized PU.1 binding site, BSAP targets a portion of the PU.1 transactivation domain (residues 7 to 30) for repression. The BSAP inhibitory domain (residues 358 to 385) is needed for this repression. Interestingly, the coactivator protein p300 can eliminate this BSAP-mediated repression. We also show that PU.1 can inhibit BSAP transactivation and that this repression requires PU.1 amino acids 7 to 30. Transfection of p300 resulted in only a partial reversal of PU.1-mediated repression of BSAP. When PU.1 function is assayed in the context of the immunoglobulin κ chain 3′ enhancer and associated binding proteins, BSAP represses PU.1 function by a distinct mechanism. This repression does not require the PU.1 transactivation or PEST domains and cannot be reversed by p300 expression. The possible roles of BSAP and PU.1 antagonistic activities in hematopoietic development are discussed.

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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.

Molecular and Cellular Biology ◽

10.1128/mcb.14.3.1786 ◽

1994 ◽

Vol 14 (3) ◽

pp. 1786-1795 ◽

Cited By ~ 138

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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