Differential binding of zinc fingers from Xenopus TFIIIA and p43 to 5S RNA and the 5S RNA gene.

Darby, Martyn K.; Joho, Keith E.

doi:10.1128/mcb.12.7.3155

Cited by 41 publications

(32 citation statements)

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“…3). The enhancement of protease cleavage following finger 9 of TFIIIA bound to 5S RNA or 5S DNA is consistent with the possibility that all nine fingers are involved in binding to either 5S RNA or 5S DNA, as suggested by Darby and Joho (9). In either RNA or DNA complexes, some zinc fingers bind more tightly than others.…”

Section: Discussionsupporting

confidence: 66%

Proteolytic footprinting of transcription factor TFIIIA reveals different tightly binding sites for 5S RNA and 5S DNA.

Bogenhagen¹

1993

Mol. Cell. Biol.

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Transcription factor MIIA (TFIA) employs an array of nine N-terminal zinc fingers to bind specifically to both 5S RNA and 5S DNA. The binding of TFIIIA to 5S RNA and 5S DNA was studied by using a protease footprinting technique. Brief treatment of free or bound TFIIIA with trypsin or chymotrypsin generated fragments which were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Fragments retaining the N terminus of TFIIIA were identified by immunoblotting with an antibody directed against the N terminus of TFIIIA. Proteolytic footprinting of TFIIIA complexed with 5S DNA derivatives reinforced other evidence that the three N-terminal zinc fingers of TFIIIA bind most tightly to 5S DNA. Proteolytic footprinting of TFIIIA in reconstituted 7S ribonucleoprotein particles revealed different patterns of trypsin sensitivity for TFIA bound to oocyte versus somatic 5S RNA. Trypsin cleaved TFIA between zinc fingers 3 and 4 more readily when the protein was bound to somatic 5S RNA than when it was bound to oocyte 5S RNA. A tryptic fragment of TFIIIA containing zinc fingers 4 through 7 remained tightly associated with somatic SS RNA. Zinc fingers 4 through 7 may represent a tightly binding site for 5S RNA in the same sense that fingers 1 through 3 represent a tightly binding site for 5S DNA.TFIIIA is a unique example of a zinc finger transcription factor that binds specifically to 5S RNA as well as to 5S DNA (20,30). TFIIIA is typically prepared from an abundant 7S storage particle from immature Xenopus laevis ovaries. Smith et al. (37) showed that TFIIIA within the 7S particle could be cleaved with proteases such as papain and trypsin to yield fragments of the protein that retained the ability to bind to the intragenic control region (ICR) of the 5S RNA gene. A 30-kDa fragment that contains nine zinc fingers provided essentially the same DNase I footprint over residues 46 to 95 of the 5S RNA gene obtained with intact TFIIIA. A 20-kDa fragment that contains the N-terminal 220 residues of TFIIIA (seven fingers) protected only the distal portion of the ICR of the 5S RNA gene from digestion by DNase I. This work provided the first clear evidence that TFIIIA binds to the ICR in an extended conformation with zinc fingers 1 through 9 aligned from the 3' to the 5' end of the ICR. This alignment leaves the carboxyl-terminal nonzinc finger domain of TFIIIA near the 5' portion of the ICR, where it appears to interact with other transcription factors (19, 37). Two groups have recently shown that aminoterminal fragments of TFIIIA containing as few as three zinc fingers bind tightly to the distal portion of the ICR (5, 25). Indeed, fingers 1 through 3 bind to gene residues 77 through 92 nearly as tightly as intact TFIIIA binds to the complete ICR. This implies that specific contacts of fingers 4 through 9 of TFIIIA with gene sequences located 5' to this tightly binding site are not as energetically favorable. Current models suggest that fingers 4 and 6 may not make tight contacts in the major groove of DNA (6,11,18 (40...

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Section: Discussionsupporting

confidence: 66%

Proteolytic footprinting of transcription factor TFIIIA reveals different tightly binding sites for 5S RNA and 5S DNA.

Bogenhagen¹

1993

Mol. Cell. Biol.

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“…The CH1 and CH2 regions of the PRP9 protein, as well as those found in three other splicing factors, the yeast PRP6, PRP 11 proteins and the human U 1 C protein, are loosely related to those found in zinc finger proteins (Legrain and Choulika 1990). The canonical TFIIIA zinc fingers are involved in DNA and RNA binding (Darby and Joho 1992;Theunissen et al 1992), but more generally, zinc fingers are considered as basic structural protein elements (Kaptein 1991). Our results strongly suggest that the CH2 motif may be directly involved in the homodimerization process but not necessarily as sites of direct contact.…”

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confidence: 99%

Interactions between PRP9 and SPP91 splicing factors identify a protein complex required in prespliceosome assembly.

Legrain¹,

Chapon²,

Galisson³

1993

Genes & Development

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The PRP9 protein is a yeast splicing factor implicated in the early steps of spliceosome assembly whose sequence contains an amino-terminal putative leucine zipper structure and two carboxy-terminal motifs reminiscent of zinc fingers. Here, we show that the deletion of the second carboxy-terminal motif results in a dominant lethal phenotype. This observation, combined with an in vivo-binding assay for protein-protein interactions, reveals the presence of two distinct binding sites on the PRP9 protein. The carboxy-terminal region contributes to the PRP9 homodimerization, whereas the amino-terminal region binds the SPP91 splicing [actor. Further experiments suggest that other factors bind to PRP9 and SPP91 proteins. Finally, we demonstrate that the PRP9 protein acts after the formation of the U1 snRNP-pre-mRNA complex. The existence of a protein complex including the PRP9 factor is discussed.[Key Words: PRP; yeast; GAL4 fusion protein; pre-mRNA splicing]

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“…These proteins are characterized by Cys 2 -His 2 zinc finger motifs often repeated in tandem that fold around zinc ions and function as nucleic acid binding domains (3)(4)(5)(6). About one-third of mammalian Cys 2 -His 2 zinc finger proteins contain a conserved domain of approximately 75 amino acids called KRAB (Kruppelassociated box) (7).…”

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confidence: 99%

Direct Interaction of the KRAB/Cys2-His2Zinc Finger Protein ZNF74 with a Hyperphosphorylated Form of the RNA Polymerase II Largest Subunit

Grondin

Côté

Bazinet

et al. 1997

Journal of Biological Chemistry

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We previously identified ZNF74 as a developmentally expressed gene commonly deleted in DiGeorge syndrome. ZNF74 encodes an RNA-binding protein tightly associated with the nuclear matrix and belongs to a large subfamily of Cys 2 -His 2 zinc finger proteins containing a KRAB (Kruppel-associated box) repressor motif. We now report on the multifunctionality of the zinc finger domain of ZNF74. This nucleic acid binding domain is shown here to function as a nuclear matrix targeting sequence and to be involved in protein-protein interaction. By far-Western analysis and coimmunoprecipitation studies, we demonstrate that ZNF74 interacts, via its zinc finger domain, with the hyperphosphorylated largest subunit of RNA polymerase II (pol IIo) but not with the hypophosphorylated form. The importance of the phosphorylation in this interaction is supported by the observation that phosphatase treatment inhibits ZNF74 binding. Double immunofluorescence experiments indicate that ZNF74 colocalizes with the pol IIo and the SC35 splicing factor in irregularly shaped subnuclear domains. Thus, ZNF74 sublocalization in nuclear domains enriched in pre-mRNA maturating factors, its RNA binding activity, and its direct phosphodependent interaction with the pol IIo, a form of the RNA polymerase functionally associated with premRNA processing, suggest a role for this member of the KRAB multifinger protein family in RNA processing.Zinc finger proteins of the TFIIIA/Kruppel type belong to the largest known family of transcription factors (1, 2). These proteins are characterized by Cys 2 -His 2 zinc finger motifs often repeated in tandem that fold around zinc ions and function as nucleic acid binding domains (3-6). About one-third of mammalian Cys 2 -His 2 zinc finger proteins contain a conserved domain of approximately 75 amino acids called KRAB (Kruppelassociated box) (7). The KRAB domain, located at the N terminus of Cys 2 -His 2 multifinger proteins, can confer strong distance-independent transcriptional repression of both activated and basal RNA polymerase II promoter activity (8 -14). Since they encode a repression motif and a potential DNA binding domain, members from the large KRAB/Cys 2 -His 2 protein family are presently thought to function as transcriptional regulators of gene expression.We previously cloned ZNF74, a gene that encodes a KRAB/ Cys 2 -His 2 protein (15). ZNF74 lies a few kilobases proximal to a polymorphic CA repeat (D22S264) (16) that was shown to be a distal marker for 22q11.2 deletions associated with increased susceptibility to schizophrenia (17). ZNF74 is also one of the few genes found hemizygously deleted in the majority of patients with the DiGeorge syndrome, a microdeletion disorder associated with a wide variety of congenital malformations including cardiac defects, thymic hypoplasia, and hypocalcemia (18 -20). To date, however, both the role of embryologically expressed ZNF74 in the DiGeorge syndrome (19) and its biochemical and cellular functions remain unclear.Although the presence of a KRAB motif and of 1...

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Differential binding of zinc fingers from Xenopus TFIIIA and p43 to 5S RNA and the 5S RNA gene.

Cited by 41 publications

References 41 publications

Proteolytic footprinting of transcription factor TFIIIA reveals different tightly binding sites for 5S RNA and 5S DNA.

Proteolytic footprinting of transcription factor TFIIIA reveals different tightly binding sites for 5S RNA and 5S DNA.

Interactions between PRP9 and SPP91 splicing factors identify a protein complex required in prespliceosome assembly.

Direct Interaction of the KRAB/Cys2-His2Zinc Finger Protein ZNF74 with a Hyperphosphorylated Form of the RNA Polymerase II Largest Subunit

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