New mode of DNA binding of multi-zinc finger transcription factors: delta EF1 family members bind with two hands to two target sites

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.

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Molecular genetics of chromosome translocations involving EWS and related family members

Physiological Genomics ◽

10.1152/physiolgenomics.1999.1.3.127 ◽

1999 ◽

Vol 1 (3) ◽

pp. 127-138 ◽

Cited By ~ 45

Author(s):

JUNGHO KIM ◽

JERRY PELLETIER

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Molecular Genetics ◽

Family Members ◽

Binding Domain ◽

Dna Binding Domain ◽

Chromosome Translocations ◽

Amino Terminal ◽

Terminal Domain ◽

Related Family

Kim, Jungho, and Jerry Pelletier. Molecular genetics of chromosome translocations involving EWS and related family members. Physiol. Genomics 1: 127–138, 1999.—Many types of sarcomas are characterized by specific chromosomal translocations that appear to result in the production of novel, tumor-specific chimeric transcription factors. Many of these show striking similarities: the emerging picture is that the amino-terminal domain of the fusion product is donated by the Ewing's sarcoma gene ( EWS) or a related member from the same gene family, whereas the carboxy-terminal domain often consists of a DNA-binding domain derived from one of a number of transcription factors. Given the observation that the different translocation partners of the EWS protooncogene are associated with distinct types of sarcomas, the functional consequence of fusing EWS (or a related family member) to a different DNA-binding domain can only be understood in the context of functional studies that define the specificity of action of the different fusion products. An understanding of the molecular structure and function of these translocations provides new methods for diagnosis and novel targets for therapeutics.

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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.

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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.

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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.

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A domain-resolution map of in vivo DNA binding reveals the regulatory consequences of somatic mutations in zinc finger transcription factors

10.1101/630756 ◽

2019 ◽

Cited By ~ 2

Author(s):

Berat Dogan ◽

Senthilkumar Kailasam ◽

Aldo Hernández Corchado ◽

Naghmeh Nikpoor ◽

Hamed S. Najafabadi

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Zinc Finger ◽

Somatic Mutations ◽

Eqtl Analysis ◽

Context Aware ◽

Dna Binding Specificity ◽

Binding Data ◽

Pan Cancer

ABSTRACTMulti-zinc finger proteins constitute the largest class of human transcription factors. Their DNA-binding specificity is usually encoded by a subset of their tandem Cys2His2 zinc finger (ZF) domains – the subset that binds to DNA, however, is often unknown. Here, by combining a context-aware machine-learning-based model of DNA recognition with in vivo binding data, we characterize the sequence preferences and the ZF subset that is responsible for DNA binding in 209 human multi-ZF proteins. We show that in vivo DNA binding is primarily driven by ∼50% of the ZFs – these DNA-binding ZFs are under strong selective pressure within and across species, and their mutations affect the expression of hundreds of genes as revealed by pan-cancer trans-eQTL analysis across 18 tissues. Among the genes affected by mutations in multi-ZF proteins, we identify several oncogenic factors regulated by SP1, and show that SP1 up-regulation in cancer promotes the expression of these genes while mutations in SP1 ZFs lead to their repression. Together, these analyses suggest that mutations in DNA-binding ZFs have distinct and widespread regulatory consequences that contribute to transcriptome remodelling in cancer.

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Self-association of the erythroid transcription factor GATA-1 mediated by its zinc finger domains.

Molecular and Cellular Biology ◽

10.1128/mcb.15.5.2448 ◽

1995 ◽

Vol 15 (5) ◽

pp. 2448-2456 ◽

Cited By ~ 122

Author(s):

M Crossley ◽

M Merika ◽

S H Orkin

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Zinc Finger ◽

Protein Interactions ◽

Physical Interaction ◽

Erythroid Cells ◽

Protein Protein Interactions ◽

Self Association ◽

Zinc Finger Region ◽

In Erythroid Cells

GATA-1, the founding member of a distinctive family of transcription factors, is expressed predominantly in erythroid cells and participates in the expression of numerous erythroid cell-expressed genes. GATA-binding sites are found in the promoters and enhancers of globin and nonglobin erythroid genes as well as in the alpha- and beta-globin locus control regions. To elucidate how GATA-1 may function in a variety of regulatory contexts, we have examined its protein-protein interactions. Here we show that GATA-1 self-associates in solution and in whole-cell extracts and that the zinc finger region of the molecule is sufficient to mediate this interaction. This physical interaction can influence transcription, as GATA-1 self-association is able to recruit a transcriptionally active but DNA-binding-defective derivative of GATA-1 to promoter-bound GATA-1 and result in superactivation. Through in vitro studies with bacterially expressed glutathione S-transferase fusion proteins, we have localized the minimal domain required for GATA-1 self-association to 40 amino acid residues within the C-terminal zinc finger region. Finally, we have detected physical interaction of GATA-1 with other GATA family members (GATA-2 and GATA-3) also mediated through the zinc finger domain. These findings have broad implications for the involvement of GATA factors in transcriptional control. In particular, the interaction of GATA-1 with itself and with other transcription factors may facilitate its function at diverse promoters in erythroid cells and also serve to bring together, or stabilize, loops between distant regulatory elements, such as the globin locus control regions and downstream globin promoters. We suggest that the zinc finger region of GATA-1, and related proteins, is multifunctional and mediates not only DNA binding but also important protein-protein interactions.

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Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages

10.1101/345835 ◽

2018 ◽

Cited By ~ 1

Author(s):

Gregory J. Fonseca ◽

Jenhan Tao ◽

Emma M. Westin ◽

Sascha H. Duttke ◽

Nathanael J. Spann ◽

...

Keyword(s):

Machine Learning ◽

Transcription Factors ◽

Dna Binding ◽

Specific Binding ◽

Family Members ◽

General Mechanism ◽

Loss Of Function ◽

Chip Sequencing ◽

Collaborative Interactions ◽

Genomic Locations

ABSTRACTMechanisms by which members of the AP-1 family of transcription factors play both redundant and non-redundant biological roles despite recognizing the same DNA sequence remain poorly understood. To address this question, we investigated the molecular functions and genome-wide DNA binding patterns of AP-1 family members in macrophages. ChIP-sequencing showed overlapping and distinct binding profiles for each factor that were remodeled following TLR4 ligation. Development of a machine learning approach that jointly weighs hundreds of DNA recognition elements yielded dozens of motifs predicted to drive factor-specific binding profiles. Machine learning-based predictions were confirmed by analysis of the effects of mutations in genetically diverse mice and by loss of function experiments. These findings provide evidence that non-redundant genomic locations of different AP-1 family members in macrophages largely result from collaborative interactions with diverse, locus-specific ensembles of transcription factors and suggest a general mechanism for encoding functional specificities of their common recognition motif.

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