Cloning the cDNA for a new human zinc finger protein defines a group of closely related krüppel like transcription factors. (1998 Nov)
cloning the cDNA for a new human zinc finger protein defines a group of closely related krüppel like transcription factors . We have identified a novel zinc finger protein that has been named ubiquitous krüppel like factor ( UKLF ) based on structural considerations and the pattern of gene expression . UKLF was isolated by the polymerase chain reaction approach using degenerate oligonucleotides corresponding to the DNA binding domain of erythroid krüppel like factor ( EKLF ) and cDNA prepared from human vascular endothelial cells . The carboxyl terminal portion of UKLF contains three zinc fingers of the Cys2 His2 type and binds in vitro to the caccc motif of the beta globin promoter and to the Sp1 recognition sequence . The amino terminal portion of UKLF consists of a hydrophobic region rich in serines and a negatively charged segment with several glutamic acid residues . The first 47 amino acids of the acidic region are nearly identical to the amino terminal portion of another krüppel like factor , the so called core promoter binding protein ( CPBP ) or Zf9 . Like CPBP / Zf9 , UKLF can function as a transcription activator in co transfection assays . however , this activity is lost when the highly conserved amino terminal segment is deleted . these findings indicate that UKLF and CPBP / Zf9 represent a distinct subgroup of closely related krüppel like activators of transcription . mapping of the UKLF gene to chromosome 2 suggested that UKLF and CPBP …

Molecular cloning of a zinc finger protein which binds to the heptamer of the signal sequence for V ( D … (1994 Jan)
molecular cloning of a zinc finger protein which binds to the heptamer of the signal sequence for V ( D ) J recombination . The somatic V ( D ) J recombination for the assembly of the Ig and TCR genes is mediated by the recombination signal sequences ( Rss ) and the V ( D ) J recombinase . A cDNA clone was isolated from a lambda gt11 expression library made from mouse thymocyte poly ( A ) RNA , using the Rss as a ligand . The deduced amino acid sequence of the putative protein , designated recognition component ( Rc ) , reveals a pair of Cys2 His2 zinc fingers followed by a Glu and Asp rich acidic domain . In addition , there are five copies of the Ser / Thr Pro X Arg / Lys sequence , which are putative DNA binding units . The zinc finger acidic domain structures present in Rc are also found in several enhancer binding proteins , such as those for the kappa B motif of the Ig kappa light chain enhancer or related sequences . bacterial fusion proteins for Rc bind preferentially to the Rss heptamer and to the kappa B motif . The dual affinities of Rc for the Rss heptamer and the kappa B motif suggest a possible link between Ig transcription and somatic recombination . The formation of multiple gel shifted DNA protein complexes for Rc and its DNA ligand suggests that these complexes tend to …

Recruitment of CD40 and tumor necrosis factor receptor associated factors 2 and 3 to membrane microdomains during CD40 signaling. (2000 Jun)
recruitment of CD40 and tumor necrosis factor receptor associated factors 2 and 3 to membrane microdomains during CD40 signaling . signals delivered to antigen presenting cells through CD40 are critical for the activation of immune responses . intracellular tumor necrosis factor ( TNF ) receptor associated factors ( trafs ) are key elements of the signal transduction pathways of many TNF receptor family members , including CD40 . We show for the first time that engagement of CD40 in intact B cells induces the rapid translocation of traf2 from the cytoplasm to the plasma membrane . We found that CD40 engagement also results in its recruitment , together with traf2 and traf3 , to membrane microdomains , regions of the plasma membrane enriched in signaling molecules such as the Src family kinases . using a membrane permeable chelator of zinc or a mutant traf2 molecule , we show that the putative zinc binding domains of trafs contribute to their recruitment to microdomains and to the downstream activation of c Jun N terminal kinase . We suggest that the zinc RING and zinc finger domains of trafs are required for communication between CD40 and microdomain associated signaling molecules and may serve a similar role in the signal transduction pathways of other TNF receptor family members .

Why zinc fingers prefer zinc : ligand field symmetry and the hidden thermodynamics of metal ion selectivity. (2004 Nov)
Why zinc fingers prefer zinc : ligand field symmetry and the hidden thermodynamics of metal ion selectivity . The zinc finger , a motif of protein nucleic acid recognition broadly conserved among eukaryotes , is a globular minidomain containing a tetrahedral metal binding site . preferential coordination of Zn ( 2 ) ( relative to Co ( 2 ) ) is proposed to reflect differences in ligand field stabilization energies ( lfses ) due to complete or incomplete occupancy of d orbitals . LFSE predicts that the preference for Zn ( 2 ) should be purely enthalpic in accord with calorimetric studies of a high affinity consensus peptide ( CP 1 ; blasie , C . A . , and Berg , J . ( 2002 ) biochemistry 41 , 15068 73 ) . despite its elegance , the general predominance of LFSE is unclear as ( i ) the magnitude by which CP 1 prefers Zn ( 2 ) is greater than that expected and ( ii ) the analogous metal ion selectivity of a zinc metalloenzyme ( carbonic anhydrase ) is driven by changes in entropy rather than enthalpy . because CP 1 was designed to optimize zinc binding , we have investigated the NMR structure and metal ion selectivity of a natural finger of lower stability derived from human tumor suppressor protein WT1 . raman spectroscopy suggests that the structure of the WT1 domain is unaffected by interchange of Zn ( 2 ) and Co ( 2 …

CDNA cloning , DNA binding , and evolution of mammalian transcription factor IIIA. (2002 Jan)
cDNA cloning , DNA binding , and evolution of mammalian transcription factor IIIA . cDNA for rat transcription factor IIIA ( tfiiia ) was cloned by degenerate PCR and rapid amplification of cDNA ends . This cDNA coded for a protein with nine Cys ( 2 ) His ( 2 ) zinc fingers and a non finger C terminal tail ; 63 amino acid ( aa ) sequence identity was observed with the xenopus tfiiia zinc finger region . recombinant rat protein containing only the nine fingers afforded dnase I protection of the identical nucleotides protected by xenopus laevis native tfiiia on the xenopus 5S RNA gene internal control region . A putative mouse tfiiia clone was identified in an expressed sequence tag database by sequence similarity to rat tfiiia . recombinant nine finger protein from this clone afforded dnase I protection of the xenopus 5S rRNA gene like the native frog protein as did a recombinant nine finger form of a putative human tfiiia clone . these DNA binding results demonstrate that these clones code for the respective mammalian tfiiias . rodent and human tfiiias share about 87 aa sequence identity in their zinc finger regions and have evolved to about the same extent as X . laevis and xenopus borealis tfiiias . A monoclonal antibody against human p53 tumor suppressor bound to rat and mouse tfiiia but not to human tfiiia in western blots . The N terminal regions of rodent and human tfiiia do not contain the …

Identification of DNA recognition sequences and protein interaction domains of the multiple Zn finger protein Roaz. (1998 Nov)
identification of DNA recognition sequences and protein interaction domains of the multiple Zn finger protein Roaz . Roaz , a rat C2H2 zinc finger protein , plays a role in the regulation of olfactory neuronal differentiation through its interaction with the Olf 1 / EBF transcription factor family . An additional role for the Roaz / Olf 1 / EBF heterodimeric protein is suggested by its ability to regulate gene activation at a distinct promoter lacking Olf 1 / EBF binding sites . using an in vitro binding site selection assay ( selex ) , we demonstrate that Roaz protein binds to novel inverted perfect or imperfect repeats of gcaccc separated by 2 bp . We show that Roaz is capable of binding to a canonical consensus recognition sequence with high affinity ( Kd 3 nM ) . analysis of the structural requirement for protein dimerization and DNA binding by Roaz reveals the role of specific zinc finger motifs in the Roaz protein for homodimerization and heterodimerization with the Olf 1 / EBF transcription factor . The DNA binding domain of Roaz is mapped to the N terminal 277 amino acids , containing the first seven zinc finger motifs , which confers weak monomeric binding to a single half site and a stronger dimeric binding to the inverted repeat in a binding site dependent manner . Full length protein can form dimers on both the inverted repeat and direct repeat but not on a single half site . these findings …

Metal and DNA binding properties and mutational analysis of the transcription activating factor , B , of coliphage 186 : … (1997 Aug)
metal and DNA binding properties and mutational analysis of the transcription activating factor , B , of coliphage 186 : a prokaryotic C4 zinc finger protein . coliphage 186 B is a 72 amino acid protein belonging to the Ogr family of analogous transcription factors present in P2 like phage , which contain a Cys X2 Cys X22 Cys X4 Cys presumptive zinc finger motif . The molecular characterization of these proteins has been hampered by their insolubility , a difficulty overcome in the present study by obtaining B as a soluble cadmium containing derivative ( CdB ) . atomic absorption spectroscopy showed the presence of one atom of cadmium per molecule of purified CdB . The UV absorption spectrum revealed a shoulder at 250 nm , characteristic of CysS Cd ( II ) ligand to metal charge transfer transitions , and the difference absorption coefficient after acidification ( delta epsilon 248 , 24 mM 1 cm 1 ) indicated the presence of a Cd ( Cys S ) 4 center . Gel mobility shift analysis of CdB with a 186 late promoter demonstrated specific DNA binding ( KD , app 3 4 microm ) and the protein was shown to activate transcription in vitro from a promoter reporter plasmid construct . The B DNA binding site was mapped by gel shift and dnaase I cleavage protection experiments to an area between 70 and 43 relative to the transcription start site , coincident with the consensus sequence , gttgt N8 …

The transactivation domain within cysteine / histidine rich region 1 of CBP comprises two novel zinc binding modules. (2000 Jun)
The transactivation domain within cysteine / histidine rich region 1 of CBP comprises two novel zinc binding modules . cAMP response element binding protein binding protein ( CBP ) is a transcriptional coactivator that interacts with a number of DNA binding proteins and cofactor proteins involved in the regulation of transcription . relatively little is known about the structure of CBP , but it has been noted that it contains three domains that are rich in cysteine and histidine ( CH1 , CH2 , and CH3 ) . The sequence of CH2 conforms to that of a leukemia associated protein domain ( PHD finger ) , and it has been postulated that this and both CH1 and CH3 may be zinc finger domains . This has not , however , been demonstrated experimentally . We have studied CH1 and show that it is composed of two novel zinc binding modules , which we term zinc bundles . Each bundle contains the sequence Cys X ( 4 ) Cys X ( 8 ) His X ( 3 ) Cys , and we show that a synthetic peptide comprising one zinc bundle from CH1 can fold in a zinc dependent manner . CH3 also appears to contain two zinc bundles , one with the variant sequence Cys X ( 2 ) Cys X ( 9 ) His X ( 3 ) Cys , and we demonstrate that this variant motif also undergoes Zn ( II ) induced folding . CH1 acts as …

A novel human striated muscle RING zinc finger protein , SMRZ , interacts with smt3b via its RING domain. (2001 Jun)
A novel human striated muscle RING zinc finger protein , SMRZ , interacts with smt3b via its RING domain . The RING domain is a conserved zinc finger motif , which serves as a protein protein interaction interface . searches of a human heart expressed sequence tag data base for genes encoding the RING domain identified a novel cDNA , named striated muscle RING zinc finger protein ( SMRZ ) . The SMRZ cDNA is 1 . 9 kilobase pairs in length and encodes a polypeptide of 288 amino acid residues ; analysis of the peptide sequence demonstrated an N terminal RING domain . fluorescence in situ hybridization localized SMRZ to chromosome 1p33 34 . northern blots demonstrated that SMRZ is expressed exclusively in striated muscle . In the cardiovascular system , SMRZ is more highly expressed in the fetal heart than in the adult heart ( slightly higher expression in the ventricle than in the atrium ) , suggesting that SMRZ is developmentally regulated . SMRZ was found to interact with smt3b , a ubiquitin like protein , through the SMRZ RING domain . This interaction was abolished by mutagenesis of conserved RING domain residues . transient transfection of SMRZ into c2c12 myoblasts showed localization of SMRZ to the nucleus . these data suggest that SMRZ may play an important role in striated muscle cell embryonic development and perhaps in cell cycle regulation .

Characterization of the thermosensitive ts453 reovirus mutant : increased dsrna binding of sigma 3 protein correlates with interferon resistance. (1998 Aug)
characterization of the thermosensitive ts453 reovirus mutant : increased dsrna binding of sigma 3 protein correlates with interferon resistance . The mutation harbored by the reovirus ts453 thermosensitive mutant has been assigned to the S4 gene encoding the major outer capsid protein sigma 3 . previous gene sequencing has identified a nonconservative amino acid substitution located near the zinc finger of sigma 3 protein in the mutant . coexpression in COS cells of the sigma 3 protein presenting this amino acid substitution ( N16K ) , together with the other major capsid protein mu 1 , has also revealed an altered interaction between the two proteins ; this altered interaction prevents the sigma 3 dependent cleavage of mu 1 to mu 1C . This could explain the lack of outer capsid assembly observed during ts453 virus infection at nonpermissive temperature . In the present study , we pursued the characterization of this mutant sigma 3 protein . although the N16K mutation is located close to the zinc finger region , it did not affect the ability of the protein to bind zinc . In contrast , this mutation , as well as mutations within the zinc finger motif itself , can increase the binding of the protein to double stranded RNA ( dsrna ) . It also appears that the N16K mutant protein is more efficiently transported to the nucleus than the wild type protein , an observation consistent with the postulated role of dsrna binding in sigma 3 nuclear …

Nucleolin modulates the subcellular localization of GDNF inducible zinc finger protein 1 and its roles in transcription and cell proliferation. (2007 Oct)
nucleolin modulates the subcellular localization of GDNF inducible zinc finger protein 1 and its roles in transcription and cell proliferation . GZF1 is a zinc finger protein induced by glial cell line derived neurotrophic factor ( GDNF ) . It is a sequence specific transcriptional repressor with a BTB / POZ ( broad complex , tramtrack , Bric a brac / poxvirus and zinc finger ) domain and ten zinc finger motifs . In the present study , we used immunoprecipitation and mass spectrometry to identify nucleolin as a GZF1 binding protein . deletion analysis revealed that zinc finger motifs 1 4 of GZF1 mediate its association with nucleolin . When zinc fingers 1 4 were deleted from GZF1 or nucleolin expression was knocked down by short interference RNA ( sirna ) , nuclear localization of GZF1 was impaired . these results suggest that nucleolin is involved in the proper subcellular distribution of GZF1 . In addition , overexpression of nucleolin moderately inhibited the transcriptional repressive activity of GZF1 whereas knockdown of nucleolin expression by sirna enhanced its activity . Thus , the repressive activity of GZF1 is modulated by the level at which nucleolin is expressed . finally , we found that knockdown of GZF1 and nucleolin expression markedly impaired cell proliferation . these findings suggest that the physiological functions of GZF1 may be regulated by the protein s association with nucleolin .

Isolation , tissue expression , and chromosomal assignment of a novel human gene which encodes a protein with RING finger … (1999 Jan)
isolation , tissue expression , and chromosomal assignment of a novel human gene which encodes a protein with RING finger motif . We identified a novel gene encoding a RING finger ( c3hc4 type zinc finger ) protein from a human neuroblastoma full length enriched cDNA library . This cDNA clone consists of 1919 nucleotides with an open reading frame of a 485 amino acid protein . From reverse transcription ( RT ) polymerase chain reaction ( PCR ) analysis , the messenger RNA was ubiquitously expressed in various human adult tissues . The chromosomal location of the gene was determined on the chromosome 6p21 . 3 region by PCR based analyses with both a human / rodent monochromosomal hybrid cell panel and a radiation hybrid mapping panel .

FYVE finger proteins as effectors of phosphatidylinositol 3 phosphate. (1999 Jun)
FYVE finger proteins as effectors of phosphatidylinositol 3 phosphate . phosphatidylinositol 3 phosphate ( ptdins ( 3 ) P ) , generated via the phosphorylation of phosphatidylinositol by phosphatidylinositol 3 kinase ( PI 3 kinase ) , plays an essential role in intracellular membrane traffic . The underlying mechanism is still not understood in detail , but the recent identification of the FYVE finger as a protein domain that binds specifically to ptdins ( 3 ) P provides a number of potential effectors for ptdins ( 3 ) P . The FYVE finger ( named after the first letter of the four proteins containing it ; fab1p , YOTB , vac1p and EEA1 ) is a double zinc binding domain that is conserved in more than 30 proteins from yeast to mammals . It is found in several proteins involved in intracellular traffic , and FYVE finger mutations that affect zinc binding are associated with the loss of function of several of these proteins . The interaction of FYVE fingers with ptdins ( 3 ) P may serve three alternative functions : first , to recruit cytosolic FYVE finger proteins to ptdins ( 3 ) P containing membranes ( in concert with accessory molecules ) ; second , to enrich for membrane bound FYVE finger proteins into ptdins ( 3 ) P containing microdomains within the membrane ; and third , to modulate the activity of membrane bound FYVE finger proteins .

Cloning and functional characterization of Roaz , a zinc finger protein that interacts with O / E 1 to regulate … (1997 Jun)
cloning and functional characterization of Roaz , a zinc finger protein that interacts with O / E 1 to regulate gene expression : implications for olfactory neuronal development . We have identified a protein , Rat O / E 1 associated zinc finger protein ( Roaz ) , that plays a role in regulating the temporal and spatial pattern of olfactory neuronal specific gene expression . This protein functions by interacting with the olfactory factor O / E 1 and modulating its transcriptional activity . Roaz , isolated via a yeast two hybrid screen , encoded a protein containing 29 C2H2 zinc fingers of the tfiiia type . The Roaz mRNA was found in brain , eye , olfactory epithelium , spleen , and heart . In situ hybridization data indicated that Roaz was expressed in the basal layer , consisting of neural precursor cells and immature sensory neurons of the olfactory epithelium , but not in the mature receptor cells . We showed that the Roaz protein bound specifically to O / E 1 by using the yeast two hybrid system . The two proteins formed a stable complex in coimmunoprecipitation and in vitro binding assays . introduction of Roaz and O / E 1 into cells containing an olfactory promoter driven luciferase reporter demonstrated that Roaz abolished O / E 1 mediated transcriptional activation . We propose that the function of Roaz is to modulate negatively the transactivational activity of O / E 1 and to act as …

From repression domains to designer zinc finger proteins : a novel strategy of intracellular immunization against HIV. (1996 Oct)
From repression domains to designer zinc finger proteins : a novel strategy of intracellular immunization against HIV . tissue specific gene regulation of eukaryotic organisms is to a large extent mediated by transcription factors that interact with genomic DNA sequences in a sequence specific manner . The purpose of this synopsis is to put forward the potential of designer zinc finger proteins in treating infections of human immunodeficiency virus ( HIV ) . artificial transcription factors containing designer zinc finger structures fused to activator or repressor domains have been designated transcription response modifiers ( TRMs ) . The principle of engineering TRMs has been derived from the analysis of human krüppel type zinc finger genes and their products . Our research efforts encompass two fascinating features that are displayed by the human krüppel type zinc finger protein KOX1 : 1 ) the krüppel type zinc finger domains display rules of sequence specific DNA recognition , and 2 ) the evolutionarily conserved krüppel associated box ( KRAB ) presents one of the strongest transcriptional repressors identified so far in mammalian organisms . The KRAB repressor activity is postulated to be mediated through co repressor molecules , such as silencing mediating protein 1 ( SMP 1 ) . Thus , the structural organization and functional analysis of zinc finger proteins revealed principles of zinc finger transcription factors that are applicable for reducing the viral load in individuals infected with HIV . In this article , a novel concept of generating therapeutic proteins …

Self association of the erythroid transcription factor GATA 1 mediated by its zinc finger domains. (1995 Jun)
Self association of the erythroid transcription factor GATA 1 mediated by its zinc finger domains . 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 . …

A xenopus zinc finger protein that specifically binds dsrna and RNA DNA hybrids. (1997 Sep)
A xenopus zinc finger protein that specifically binds dsrna and RNA DNA hybrids . proteins containing C2H2 type zinc finger motifs represent one of the largest classes of nucleic acid binding proteins found in nature . We describe a novel zinc finger protein , dsrbp ZFa , isolated by screening an expression library with dsrna . The dsrbp ZFa cDNA encodes a protein containing seven zinc finger motifs and an acidic C terminal domain . mobility shift experiments demonstrate that dsrbp ZFa binds dsrna and RNA DNA hybrids with nanomolar dissociation constants and in a sequence independent manner . We also show that DNA and single stranded RNA fail to compete with dsrna for binding suggesting dsrbp ZFa prefers to bind an A form helix . using western analyses we have localized dsrbp ZFa primarily to the nucleus of xenopus laevis oocytes . The identification of dsrbp ZFa provides the first example of a zinc finger protein that is specific for dsrna . In addition , dsrbp ZFa does not contain the previously described dsrna binding motif , suggesting certain zinc fingers may provide an alternative way to recognize the A form helix .

Effect of redox conditions on the DNA binding efficiency of the retinoic acid receptor zinc finger. (1998 Dec)
effect of redox conditions on the DNA binding efficiency of the retinoic acid receptor zinc finger . retinoic acid and its derivatives are involved in many important biological processes . In the present study , we have shown that the DNA binding domain of the retinoic acid receptor , which contains two zinc fingers with the Zn ( II ) tetrahedrally coordinated by four Cys , is susceptible to intracellularly relevant oxidizing agents . In the presence of hydrogen peroxide or hypochlorite , the zinc finger DNA binding activity was abolished in a concentration dependent manner . The loss of DNA binding activity was correlated with the release of Zn ( II ) from the zinc finger motif as a consequence of Zn ( II ) thiolate bond oxidation . A combination of glutathione and Zn ( II ) was able to restore the activity , suggesting that oxidation of the zinc finger by hydrogen peroxide or hypochlorite resulted in the formation of disulfide bonds between the Cys present in the Zn ( II ) binding motif . Our results indicate that in situations of oxidative stress zinc finger containing transcription factors may be particularly susceptible to oxidation , resulting in the disruption of control and regulation of gene expression .

Treble clef finger a functionally diverse zinc binding structural motif. (2001 Apr)
treble clef finger a functionally diverse zinc binding structural motif . detection of similarity is particularly difficult for small proteins and thus connections between many of them remain unnoticed . structure and sequence analysis of several metal binding proteins reveals unexpected similarities in structural domains classified as different protein folds in SCOP and suggests unification of seven folds that belong to two protein classes . The common motif , termed treble clef finger in this study , forms the protein structural core and is 25 45 residues long . The treble clef motif is assembled around the central zinc ion and consists of a zinc knuckle , loop , beta hairpin and an alpha helix . The knuckle and the first turn of the helix each incorporate two zinc ligands . treble clef domains constitute the core of many structures such as ribosomal proteins L24E and S14 , RING fingers , protein kinase cysteine rich domains , nuclear receptor like fingers , LIM domains , phosphatidylinositol 3 phosphate binding domains and His Me finger endonucleases . The treble clef finger is a uniquely versatile motif adaptable for various functions . This small domain with a 25 residue structural core can accommodate eight different metal binding sites and can have many types of functions from binding of nucleic acids , proteins and small molecules , to catalysis of phosphodiester bond hydrolysis . treble clef motifs are frequently incorporated in larger structures or occur in doublets . present analysis suggests that the …

Recent developments in the engineering of zinc finger proteins. (2004 Jul)
recent developments in the engineering of zinc finger proteins . within the last 20 years , the understanding of the biology of the classical or Cys ( 2 ) His ( 2 ) zinc finger domain has progressed rapidly from the initial identification of the zinc finger as a repetitive zinc binding motif in transcription factors to its use in biotechnology . The domain is the most abundant DNA binding motif in the human genome and is a component of many key eukaryotic transcription factors involved in growth and development . numerous structures now exist for this domain and its mode of action is known in a variety of zinc finger DNA complexes . application of this knowledge has led to the development of designer transcription factors where zinc fingers have been engineered to bind desired DNA sequences . recently , advances have been made in this field that potentially allow the targeting of any DNA site . consideration of chromatin structure and the use of effector domains in these designer transcription factors have made possible the regulation of a number of endogenous genes . these advances in the customised regulation of genes will be discussed in detail , as well as the potential to use these proteins in functional genomics and gene therapy applications .