Full length cDNA sequence encoding a nuclease-sensitive element DNA binding protein

Kolluri, Rukmini; Kinniburgh, Alan J.

doi:10.1093/nar/19.17.4771

Cited by 30 publications

(20 citation statements)

References 3 publications

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“…On the basis of its interaction with a binding site in the human papillomavirus type 18 enhancer, it was concluded that the protein bound specifically to the sense strand of this site (65). Similar studies with the closely related protein NSEP-1, whose amino acid sequence has been reported to differ from that of YB-1 in two locations in the COOH-terminal region and at the NH2 terminus, also detected preferential binding to one strand of a number of binding sites (37,38). On the basis of this study, the determining factor in strand selection appeared to be strong purine-pyrimidine asymmetry that has been shown to promote formation of H-DNA, a triplex structure which results in displacement of a pyrimidine-rich single-stranded region (23).…”

Section: Resultsmentioning

confidence: 62%

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Cloning and characterization of chicken YB-1: regulation of expression in the liver.

Grant¹,

Deeley²

1993

Mol. Cell. Biol.

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A cDNA expression library constructed from day 9 embryonic liver was screened with a previously identified protein binding site in the flanking region of the liver-specific, estrogen-dependent avian apoVLDLII gene. Two of the clones isolated were shown to encode the chicken homolog of the Y-box binding protein, YB-1 (dbpb), which we have designated chkYB-1. This protein was originally identified in avian extracts by virtue of its ability to bind to two reverse CCAAT motifs in the Rous sarcoma virus enhancer. Since its identification, additional nucleic acid binding properties have been ascribed to its homologs, or closely related proteins, in other species. We have determined the sequence of chkYB-1, investigated its ability to bind to sites known to be involved in tissue-specific expression in the liver, and examined factors influencing its hepatic expression. These studies have demonstrated that the level of chkYB-1 mRNA in the liver decreases steadily throughout embryogenesis and for several weeks posthatching until adult levels are attained. We present several lines of evidence that YB-1 expression in the liver is positively associated with DNA synthesis or cell proliferation. Its binding characteristics indicate that the protein can interact specifically with a number of binding sites for liver!-enriched or specific factors. In addition, although it is not particularly asymmetric in terms of base composition, we find a marked preference in binding to the pyrimidine-rich strand of these sites regardless of the presence or polarity of an intact CCAAT box. The increased levels of expression of YB-1 during proliferation combined with its binding characteristics suggest that it may be involved in the reduced expression of liver-specific genes observed at early stages of development or during liver regeneration.A large number of elements involved in the regulation of eukaryotic genes contain a variation of the motif CCAAT as a subsequence (33). Sites containing such motifs have been shown to be recognized by a number of different trans-acting factors, some of which display restricted tissue distribution and others of which are ubiquitous (2, 44). A requirement for sequences in addition to the CCAAT motif has been demonstrated for some factors, but others display an ability to bind an array of sites with apparently little structural similarity other than the motif itself (9,18,19,29,39,61). A particularly striking example of the latter group is provided by the avian factor EFla, which was initially identified in crude nuclear protein extracts by virtue of its ability to bind to a site in the Rous sarcoma virus (RSV) long terminal repeat (LTR) (21,29,51,62). This protein has been purified and shown to bind to sites in the RSV LTR either as a homodimer or as a heterodimer formed with a second protein designated EFlb. Subsequently, EFla was shown to be capable of interacting with a number of binding sites for trans-acting factors that contain the sequence CCAAT in the noncoding DNA strand.DNA binding proteins that ha...

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Section: Resultsmentioning

confidence: 62%

“…We have also included the sequence of human NSEP, since it is unclear whether it is identical to dbpb (YB-1) (37). The sequence of the chicken protein displays a high degree of homology with the human dbpb (YB-1) sequence in regions that differ significantly from the sequence of human NSEP-1 (Fig.…”

Section: Resultsmentioning

confidence: 99%

Cloning and characterization of chicken YB-1: regulation of expression in the liver.

Grant¹,

Deeley²

1993

Mol. Cell. Biol.

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“…A growing list of proteins has been shown to bind to c-myc promoter sequences in single-stranded conformation. In addition to hnRNP K, these proteins include pur (Ϫ1700) (3), MSSP-1 (Ϫ2000) (51), far upstream binding protein (FBP) (Ϫ1525) (19), and NSEP-1 (Ϫ130) (40). Furthermore, the FBP binding region was shown to have single-stranded character in vivo, as assessed by KMnO 4 reactivity (19).…”

Section: Resultsmentioning

confidence: 99%

“…In addition to hnRNP K, several different candidates have been proposed as the factor(s) that actually mediates CT activation, including nm23 (56), NSEP-1 (40), and Sp1 (15). Data directly linking most of these factors with specific CT-mediated activation are lacking.…”

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confidence: 99%

Heterogeneous Nuclear Ribonucleoprotein K Is a Transcription Factor

Michelotti

Aronsohn

et al. 1996

Molecular and Cellular Biology

327

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The CT element is a positively acting homopyrimidine tract upstream of the c-myc gene to which the well-characterized transcription factor Sp1 and heterogeneous nuclear ribonucleoprotein (hnRNP) K, a less well-characterized protein associated with hnRNP complexes, have previously been shown to bind. The present work demonstrates that both of these molecules contribute to CT element-activated transcription in vitro. The pyrimidine-rich strand of the CT element both bound to hnRNP K and competitively inhibited transcription in vitro, suggesting a role for hnRNP K in activating transcription through this single-stranded sequence. Direct addition of recombinant hnRNP K to reaction mixtures programmed with templates bearing singlestranded CT elements increased specific RNA synthesis. If hnRNP K is a transcription factor, then interactions with the RNA polymerase II transcription apparatus are predicted. Affinity columns charged with recombinant hnRNP K specifically bind a component(s) necessary for transcription activation. The depleted factors were biochemically complemented by a crude TFIID phosphocellulose fraction, indicating that hnRNP K might interact with the TATA-binding protein (TBP)-TBP-associated factor complex. Coimmunoprecipitation of a complex formed in vivo between hnRNP K and epitope-tagged TBP as well as binding in vitro between recombinant proteins demonstrated a protein-protein interaction between TBP and hnRNP K. Furthermore, when the two proteins were overexpressed in vivo, transcription from a CT element-dependent reporter was synergistically activated. These data indicate that hnRNP K binds to a specific cis element, interacts with the RNA polymerase II transcription machinery, and stimulates transcription and thus has all of the properties of a transcription factor.

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“…The lack of suGF1 binding to single-stranded DNA (13) suggests that suGFl differs from factors proposed to stabilize unusual structures by binding to single-stranded regions (6,24). Although it is possible that a triple-helix structure is assumed by the region of the G string in vivo under localized superhelical stress in the absence of a nucleosome and plays a regulatory role by excluding suGFl from binding, we have not investigated this experimentally.…”

Section: Resultsmentioning

confidence: 99%

suGF1 binds in the major groove of its oligo(dG).oligo(dC) recognition sequence and is excluded by a positioned nucleosome core.

Patterton

Hapgood

1994

Mol. Cell. Biol.

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We have elsewhere reported the purification of a poly(dG) poly(dC)-binding nuclear protein (suGFl) from sea urchin embryos (J. Hapgood and D. Patterton, Mol. Cell. Biol. 14:this issue, 1994). We proposed that suGFl may be a member of a family of G-string factors involved in developmental gene regulation, possibly via alterations in chromatin structure. In this article, we characterize the binding of purified suGFl to 11 contiguous Gs in the H1-H4 intergenic region of a sea urchin early histone gene battery in vitro. It is shown that suGFl-DNA binding is dependent on ionic strength and requires divalent cations. Purified suGFl forms discrete protein-DNA multimers, consistent with suGFl-suGFl interactions. In a model for the suGFl-DNA complex derived from our footprinting and methylation interference data, suGFl contacts the Gs in the major groove as well as one of the bordering phosphate backbones. The data are consistent with the direction of curvature of the DNA in the suGFl-DNA complex being the same as that preferred by the free DNA and exhibited by the DNA when bent around a positioned nucleosome core in vitro. However, on the basis of steric considerations, the binding of suGFl and that of the histone octamer are predicted to be mutually exclusive.We show that suGFl is indeed unable to bind to the G string when occupied by a histone octamer located in the major in vitro positioning frame in the H1-H4 intergenic region.

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Full length cDNA sequence encoding a nuclease-sensitive element DNA binding protein

Cited by 30 publications

References 3 publications

Cloning and characterization of chicken YB-1: regulation of expression in the liver.

Cloning and characterization of chicken YB-1: regulation of expression in the liver.

Heterogeneous Nuclear Ribonucleoprotein K Is a Transcription Factor

suGF1 binds in the major groove of its oligo(dG).oligo(dC) recognition sequence and is excluded by a positioned nucleosome core.

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