On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

ABSTRACTCis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. However, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict these DNA-binding preferences. We combine information from crystal structures composed by C2H2-ZF domains and from bacterial one-hybrid experiments to compute scores for protein-DNA binding based on statistical potentials. We apply the scores to compute theoretical position weight matrices (PWMs) of proteins with a DNA-binding domain composed by C2H2-ZF domains, with the only requirement of an input structure (experimentally determined or modelled). We have tested the capacity to predict PWMs of zinc finger domains, successfully predicting 3-2 nucleotides of a trinucleotide binding site for about 70% variants of single zinc-finger domains of Zif268. We have also tested the capacity to predict the PWMs of proteins composed by three C2H2-ZF domains, successfully matching between 60% and 90% of the binding-site motif according to the JASPAR database. The tests are used as a proof of the capacity to scan a DNA fragment and find the potential binding sites of transcription-factors formed by C2H2-ZF domains. As an example, we have tested the approach to predict the DNA-binding preferences of the human chromatin binding factor CTCF.

Download Full-text

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa046 ◽

2020 ◽

Vol 2 (3) ◽

Author(s):

Alberto Meseguer ◽

Filip Årman ◽

Oriol Fornes ◽

Ruben Molina-Fernández ◽

Jaume Bonet ◽

...

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Binding Site ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Computational Method ◽

Chromatin Binding ◽

Input Structure ◽

Binding Factor ◽

Potential Binding

Abstract Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. To date, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict their DNA-binding preferences. We have computed theoretical position weight matrices (PWMs) of proteins composed by C2H2-ZF domains, with the only requirement of an input structure. We have predicted more than two-third of a single zinc-finger domain binding site for about 70% variants of Zif268, a classical member of this family. We have successfully matched between 60 and 90% of the binding-site motif of examples of proteins composed by three C2H2-ZF domains in JASPAR, a standard database of PWMs. The tests are used as a proof of the capacity to scan a DNA fragment and find the potential binding sites of transcription-factors formed by C2H2-ZF domains. As an example, we have tested the approach to predict the DNA-binding preferences of the human chromatin binding factor CTCF. We offer a server to model the structure of a zinc-finger protein and predict its PWM.

Download Full-text

Analysis of DNA Binding by a Eubacterial Zinc Finger Transcription Factor

Journal of Bacteriology ◽

10.1128/jb.00193-09 ◽

2009 ◽

Vol 191 (14) ◽

pp. 4513-4521 ◽

Cited By ~ 1

Author(s):

Victor J. McAlister ◽

Gail E. Christie

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Binding Site ◽

Zinc Finger ◽

Specific Binding ◽

Dna Interaction ◽

Late Gene ◽

Major Groove ◽

Late Gene Expression ◽

Zinc Finger Transcription Factor

ABSTRACT The Serratia marcescens NucC protein is structurally and functionally homologous to the P2 Ogr family of eubacterial zinc finger transcription factors required for late gene expression in P2- and P4-related bacteriophages. These activators exhibit site-specific binding to a conserved DNA sequence, TGT-N3-R-N4-Y-N3-aCA, that is located upstream of NucC-dependent S. marcescens promoters and the late promoters of P2-related phages. In this report we describe the interactions of NucC with the P2 FETUD late operon promoter P F . NucC is shown to bind P F as a tetramer and to make 12 symmetrical contacts to the DNA phosphodiester backbone. The backbone contacts are centered on the TGT-N3-R-N4-Y-N3-aCA motif. Major groove base contacts can be seen at most positions within the ∼24-bp binding site. Minor groove contacts map to adjacent positions in the downstream half of the binding site, which corresponds to the area in which the DNA also appears to be bent by NucC binding. NucC binding provides a new example of protein-DNA interaction that is strikingly different from the DNA binding demonstrated for eukaryotic zinc-finger transcription factors.

Download Full-text

Toward rules relating zinc finger protein sequences and DNA binding site preferences.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.89.16.7345 ◽

1992 ◽

Vol 89 (16) ◽

pp. 7345-7349 ◽

Cited By ~ 144

Author(s):

J. R. Desjarlais ◽

J. M. Berg

Keyword(s):

Dna Binding ◽

Binding Site ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Protein Sequences ◽

Site Preferences ◽

Finger Protein ◽

Dna Binding Site

Download Full-text

Determination of DNA binding specificities of mutated zinc finger domains

FEBS Letters ◽

10.1016/0014-5793(91)80545-e ◽

1991 ◽

Vol 283 (1) ◽

pp. 23-26 ◽

Cited By ~ 11

Author(s):

Hans-Jürgen Thiesen ◽

Christian Bach

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Zinc Finger Domains

Download Full-text

The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0810003106 ◽

2009 ◽

Vol 106 (17) ◽

pp. 6933-6938 ◽

Cited By ~ 34

Author(s):

Ilaria Baglivo ◽

Luigi Russo ◽

Sabrina Esposito ◽

Gaetano Malgieri ◽

Mario Renda ◽

...

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Coordination Sphere ◽

Zinc Ion ◽

Binding Domain ◽

Hydrophobic Core ◽

Zinc Finger Domain ◽

High Sequence Identity ◽

Zinc Coordination ◽

Zinc Finger Domains

The recent characterization of the prokaryotic Cys2His2 zinc-finger domain, identified in Ros protein from Agrobacterium tumefaciens, has demonstrated that, although possessing a similar zinc coordination sphere, this domain is structurally very different from its eukaryotic counterpart. A search in the databases has identified ≈300 homologues with a high sequence identity to the Ros protein, including the amino acids that form the extensive hydrophobic core in Ros. Surprisingly, the Cys2His2 zinc coordination sphere is generally poorly conserved in the Ros homologues, raising the question of whether the zinc ion is always preserved in these proteins. Here, we present a functional and structural study of a point mutant of Ros protein, Ros56–142C82D, in which the second coordinating cysteine is replaced by an aspartate, 5 previously-uncharacterized representative Ros homologues from Mesorhizobium loti, and 2 mutants of the homologues. Our results indicate that the prokaryotic zinc-finger domain, which in Ros protein tetrahedrally coordinates Zn(II) through the typical Cys2His2 coordination, in Ros homologues can either exploit a CysAspHis2 coordination sphere, previously never described in DNA binding zinc finger domains to our knowledge, or lose the metal, while still preserving the DNA-binding activity. We demonstrate that this class of prokaryotic zinc-finger domains is structurally very adaptable, and surprisingly single mutations can transform a zinc-binding domain into a nonzinc-binding domain and vice versa, without affecting the DNA-binding ability. In light of our findings an evolutionary link between the prokaryotic and eukaryotic zinc-finger domains, based on bacteria-to-eukaryota horizontal gene transfer, is discussed.

Download Full-text

Evi-1, a murine zinc finger proto-oncogene, encodes a sequence-specific DNA-binding protein.

Molecular and Cellular Biology ◽

10.1128/mcb.11.5.2665 ◽

1991 ◽

Vol 11 (5) ◽

pp. 2665-2674 ◽

Cited By ~ 69

Author(s):

A S Perkins ◽

R Fishel ◽

N A Jenkins ◽

N G Copeland

Keyword(s):

Dna Binding ◽

Binding Site ◽

Zinc Finger ◽

Sequence Data ◽

Binding Protein ◽

Consensus Sequence ◽

Dna Binding Protein ◽

Polymerase Chain Reaction Method ◽

Nucleotide Sequence Data ◽

Carboxy Terminal

Evi-1 was originally identified as a common site of viral integration in murine myeloid tumors. Evi-1 encodes a 120-kDa polypeptide containing 10 zinc finger motifs located in two domains 380 amino acids apart and an acidic domain located carboxy terminal to the second set of zinc fingers. These features suggest that Evi-1 is a site-specific DNA-binding protein involved in the regulation of RNA transcription. We have purified Evi-1 protein from E. coli and have employed a gel shift-polymerase chain reaction method using random oligonucleotides to identify a high-affinity binding site for Evi-1. The consensus sequence for this binding site is TGACAAGATAA. Evi-1 protein specifically protects this motif from DNase I digestion. By searching the nucleotide sequence data bases, we have found this binding site both in sequences 5' to genes in putative or known regulatory regions and within intron sequences.

Download Full-text

Regulation of Cell Cycle Transcription Factor Swi4 through Auto-Inhibition of DNA Binding

Molecular and Cellular Biology ◽

10.1128/mcb.19.10.6729 ◽

1999 ◽

Vol 19 (10) ◽

pp. 6729-6741 ◽

Cited By ~ 26

Author(s):

Kristin Baetz ◽

Brenda Andrews

Keyword(s):

Cell Cycle ◽

Transcription Factors ◽

Dna Binding ◽

Binding Domain ◽

Terminal Region ◽

Full Length ◽

Intramolecular Interactions ◽

Dna Binding Domain ◽

C Terminus ◽

Binding Factor

ABSTRACTInSaccharomyces cerevisiae, two transcription factors, SBF (SCB binding factor) and MBF (MCB binding factor), promote the induction of gene expression at the G1/S-phase transition of the mitotic cell cycle. Swi4 and Mbp1 are the DNA binding components of SBF and MBF, respectively. The Swi6 protein is a common subunit of both transcription factors and is presumed to play a regulatory role. SBF binding to its target sequences, the SCBs, is a highly regulated event and requires the association of Swi4 with Swi6 through their C-terminal domains. Swi4 binding to SCBs is restricted to the late M and G1phases, when Swi6 is localized to the nucleus. We show that in contrast to Swi6, Swi4 remains nuclear throughout the cell cycle. This finding suggests that the DNA binding domain of Swi4 is inaccessible in the full-length protein when not complexed with Swi6. To explore this hypothesis, we expressed Swi4 and Swi6 in insect cells by using the baculovirus system. We determined that partially purified Swi4 cannot bind SCBs in the absence of Swi6. However, Swi4 derivatives carrying point mutations or alterations in the extreme C terminus were able to bind DNA or activate transcription in the absence of Swi6, and the C terminus of Swi4 inhibited Swi4 derivatives from binding DNA intrans. Full-length Swi4 was determined to be monomeric in solution, suggesting an intramolecular mechanism for auto-inhibition of binding to DNA by Swi4. We detected a direct in vitro interaction between a C-terminal fragment of Swi4 and the N-terminal 197 amino acids of Swi4, which contain the DNA binding domain. Together, our data suggest that intramolecular interactions involving the C-terminal region of Swi4 physically prevent the DNA binding domain from binding SCBs. The interaction of the carboxy-terminal region of Swi4 with Swi6 alleviates this inhibition, allowing Swi4 to bind DNA.

Download Full-text

A New Coactivator Function for Zac1's C2H2 Zinc Finger DNA-Binding Domain in Selectively Controlling PCAF Activity

Molecular and Cellular Biology ◽

10.1128/mcb.00842-08 ◽

2008 ◽

Vol 28 (19) ◽

pp. 6078-6093 ◽

Cited By ~ 16

Author(s):

Anke Hoffmann ◽

Dietmar Spengler

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Zinc Finger ◽

Transcriptional Control ◽

Zinc Finger Protein ◽

Embryonic Stem ◽

Binding Domain ◽

Dna Binding Domain ◽

Histone H4 ◽

Histone H4 Acetylation

ABSTRACT The generally accepted paradigm of transcription by regulated recruitment defines sequence-specific transcription factors and coactivators as separate categories that are distinguished by their abilities to bind DNA autonomously. The C2H2 zinc finger protein Zac1, with an established role in canonical DNA binding, also acts as a coactivator. Commensurate with this function, p73, which is related to p53, is here shown to recruit Zac1, together with the coactivators p300 and PCAF, to the p21Cip1 promoter during the differentiation of embryonic stem cells into neurons. In the absence of autonomous DNA binding, Zac1's zinc fingers stabilize the association of PCAF with p300, suggesting its scaffolding function. Furthermore, Zac1 regulates the affinities of PCAF substrates as well as the catalytic activities of PCAF to induce a selective switch in favor of histone H4 acetylation and thereby the efficient transcription of p21Cip1. These results are consistent with an authentic coactivator function of Zac1's C2H2 zinc finger DNA-binding domain and suggest coactivation by sequence-specific transcription factors as a new facet of transcriptional control.

Download Full-text

Isolation and Functional Characterization of cDNA of Serum Amyloid A-Activating Factor That Binds to the Serum Amyloid A Promoter

Molecular and Cellular Biology ◽

10.1128/mcb.18.12.7327 ◽

1998 ◽

Vol 18 (12) ◽

pp. 7327-7335 ◽

Cited By ~ 33

Author(s):

Alpana Ray ◽

Bimal K. Ray

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Zinc Finger ◽

Okadaic Acid ◽

Serum Amyloid A ◽

Kinase Inhibitor ◽

Functional Characterization ◽

Serum Amyloid ◽

Specific Expression ◽

Amyloid A

ABSTRACT Serum amyloid A (SAA), a plasma protein inducible in response to many inflammatory conditions, is associated with the pathogenesis of several diseases including reactive amyloidosis, rheumatoid arthritis, and atherosclerosis. We have previously reported an element of the SAA promoter, designated SAA-activating sequence (SAS), that is involved in the inflammation-induced SAA expression, and a nuclear factor, SAS-binding factor (SAF), that interacts with the SAS element has been identified previously (A. Ray and B. K. Ray, Mol. Cell. Biol. 16:1584–1594, 1996). To evaluate how SAF is involved in SAA promoter activation, we have investigated structural features and functional characteristics of this transcription factor. Our studies indicate that SAF belongs to a family of transcription factors characterized by the presence of multiple zinc finger motifs of the Cys2-His2 type at the carboxyl end. Of the three cloned SAF cDNAs (SAF-1, SAF-5, and SAF-8), SAF-1 isoform showed a high degree of homology to MAZ/ZF87/Pur-1 protein while SAF-5 and SAF-8 isoforms are unique and are related to SAF-1/MAZ/ZF87/Pur-1 at the zinc finger domains but different elsewhere. Although structurally distinct, all members are capable of activating SAS element-mediated expression and display virtually identical sequence specificities. However, varying levels of expression of members of this gene family were observed in different tissues. Functional activity of SAF is regulated by a posttranslational event as SAF DNA-binding and transactivation abilities are increased by a protein phosphatase inhibitor, okadaic acid, and inhibited by a protein kinase inhibitor, H7. Consistent with this observation, increased DNA binding of the cloned SAF and its hyperphosphorylation, in response to okadaic acid treatment of the transfected cells, were observed. Taken together, our results suggest that, in addition to tissue-specific expression, SAFs, a family of zinc finger transcription factors, undergo a modification by a posttranslational event that confers their SAA promoter-binding activity and transactivation potential.

Download Full-text