Architecture of High Mobility Group Protein I-C·DNA Complex and Its Perturbation upon Phosphorylation by Cdc2 Kinase

Schwanbeck, Ralf; Manfioletti, Guidalberto; Wiśniewski, Jacek R.

doi:10.1074/jbc.275.3.1793

Cited by 38 publications

(48 citation statements)

References 52 publications

(51 reference statements)

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“…Samples were applied to a sequencing gel and scanned as described above. The quantitative analysis of the footprints was essentially carried out as described previously (37,38) with minor changes using ImageQuant 5.2 (Amersham Biosciences). Briefly, fluorescence intensities along the lanes were scanned (lines, 21-pixel width) and imported into the ALIGN software (gift from Dr. T. Heyduk, St. Louis, MO; available on request) to correct distortions of the gel.…”

Section: Methodsmentioning

confidence: 99%

Spatial Contacts and Nucleosome Step Movements Induced by the NURF Chromatin Remodeling Complex

Schwanbeck

Xiao

2004

Journal of Biological Chemistry

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131

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The nucleosome remodeling factor NURF is a foursubunit, ISWI-containing chromatin remodeling complex that catalyzes nucleosome sliding in an ATP-dependent fashion, thereby modulating the accessibility of the DNA. To elucidate the mechanism of nucleosome sliding, we have investigated by hydroxyl radical footprinting how NURF makes initial contact with a nucleosome positioned at one end of a DNA fragment. NURF binds to two separate locations on the nucleosome: a continuous stretch of linker DNA up to the nucleosome entry site and a region asymmetrically surrounding the nucleosome dyad within the minor grooves, close to residues of the histone H4 tail that have been implicated in the activation of ISWI activity. Kinetic analysis reveals that nucleosome sliding occurs in apparent increments or steps of 10 bp. Furthermore, single nucleoside gaps as well as nicks about two helical turns before the dyad interfere with sliding, indicating that structural stress at this region assists the relative movement of DNA. These findings support a sliding model in which the position-specific tethering of NURF forces a translocating ISWI ATPase to pump a DNA distortion over the histone octamer, thereby changing the translational position of the nucleosome.

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Section: Methodsmentioning

confidence: 99%

Spatial Contacts and Nucleosome Step Movements Induced by the NURF Chromatin Remodeling Complex

Schwanbeck

Xiao

2004

Journal of Biological Chemistry

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131

125

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“…The approximate average length of this DNA was 5000 bp. The 34-bp fragment of the promoter of the IFN␤ gene containing the PRDIII-1, PRDII, and NRDI elements was prepared from synthetic oligonucleotides (32,33). Four-way junction DNA (4H DNA) was prepared according to Bianchi (36).…”

Section: Methodsmentioning

confidence: 99%

“…Hydroxyl Radical DNA Footprinting-10,000 -15,000 cpm 5Ј-labeled IFN␤-DNA (30 nM) was partially digested with hydroxyl radicals in a 10-l reaction volume in presence or absence of 30 nM HMG protein in 180 mM NaCl, 20 ng/l bovine serum albumin, and 10 mM MOPS buffer, pH 7.2, at room temperature for 20 min as described previously (33). The reaction products were separated on 18% polyacrylamide sequencing gels containing 7 M urea/TBE.…”

Section: Architecture Of the Hmgi/y⅐dna Complexesmentioning

confidence: 99%

“…Application of the protein-footprinting method for mapping of protein regions interacting with DNA (31) allowed more detailed characterization of the binding of HMGI(Y) proteins to DNA (32). A combination of this method with other biochemical approaches has recently brought insights into the organization of the complex of the HMGI-C protein with a promoter region of the interferon-␤ (IFN␤) gene (33). That work revealed, that the first and the second AT-hook of the HMGI-C protein interact with PRDII and NRDI elements of the promoter (33) and that phosphorylation by Cdc2 kinase of HMGI-C perturbs organization of the protein⅐DNA complex.…”

mentioning

confidence: 99%

“…A combination of this method with other biochemical approaches has recently brought insights into the organization of the complex of the HMGI-C protein with a promoter region of the interferon-␤ (IFN␤) gene (33). That work revealed, that the first and the second AT-hook of the HMGI-C protein interact with PRDII and NRDI elements of the promoter (33) and that phosphorylation by Cdc2 kinase of HMGI-C perturbs organization of the protein⅐DNA complex. In this work we have extended our studies for other three members of the HMGI/Y family: the HMGI and HMGY as well as the insect cHMGI protein.…”

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confidence: 99%

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Distinct Organization of DNA Complexes of Various HMGI/Y Family Proteins and Their Modulation upon Mitotic Phosphorylation

Piekiełko¹,

Drung²,

Rogalla³

et al. 2001

Journal of Biological Chemistry

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High mobility group (HMG) proteins HMGI, HMGY, HMGI-C, and Chironomus HMGI are DNA-binding proteins thought to modulate the assembly and the function of transcriptional complexes. Each of these proteins contains three DNA-binding domains (DBD), properties of which appear to be regulated by phosphorylation. High levels of these proteins are characteristic for rapidly dividing cells in embryonic tissues and tumors. On the basis of their occurrence, specific functions for each of these proteins have been postulated. In this study we demonstrate differences in the nature of contacts of these proteins with promoter region of the interferon-␤ gene. We show that HMGI and HMGY interact with this DNA via three DBDs, whereas HMGI-C and Chironomus HMGI bind to this DNA using only two domains. Phos- Despite continuously increasing interest in the function(s) of this group of proteins, the nature of the interaction of these proteins with DNA is still not sufficiently understood. The proteins of the HMGI/Y family are 10 -11 kDa in size, are highly charged, are rich both in acidic and basic residues, are proline-rich, and contain only few residues with bulky hydrophobic side chains. This unusual amino acid composition inhibits folding of the polypeptide backbone of these proteins into any defined secondary structure. Common for HMGI/Y proteins is the presence of three putative DNA-binding domains (DBD), so called . NMR analysis of a complex of a peptide derived from HMGI(Y) bound to a short DNA fragment revealed that the centrally located RGR residues are essentially for binding and responsible for contacts of the protein with the bases and phosphate-sugar backbone (27). Alternative approaches, which used deletion and point-mutated proteins, revealed that two or three DBDs of the protein bind to DNA in a cooperative way (28 -30). Application of the protein-footprinting method for mapping of protein regions interacting with DNA (31) allowed more detailed characterization of the binding of HMGI(Y) proteins to DNA (32). A combination of this method

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Ectopic sequences from truncated HMGIC in liposarcomas are derived from various amplified chromosomal regions

Meza‐Zepeda

Berner

Henriksen

et al. 2001

Genes Chromosomes & Cancer

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The HMGIC gene codes for an architectural transcription factor frequently rearranged by translocation in lipomas and other benign mesenchymal tumors. In sarcomas, malignant tumors of mesenchymal origin, the gene is also found to be rearranged, but in addition amplified and overexpressed. Here we report the sequence, chromosomal localization, and expression patterns of 11 novel ectopic sequences fused to exons 2 and 3 of HMGIC in seven different sarcoma samples. In addition, we identified a number of variant transcripts observed previously in benign tumors. Consistent with the suggested role of HMGIC in adipocytic differentiation, most of the novel ectopic sequences were observed in well-differentiated liposarcomas. These tumors are known to have complex marker chromosomes containing amplified segments from several chromosomes. Five novel sequences were derived from 12q14-q15, where HMGIC resides, two from 1q24, a region frequently amplified in these types of tumors, two from 11q14, and one from chromosome 2. All except one of the aberrant transcripts encoded truncated proteins with intact DNA-binding domains (AT hooks) but lacking the C-terminal acidic region, a target for constitutive phosphorylation by protein kinase CK2. Some of the ectopic sequences were transcribed in other tissues, and most of the ectopic sequences also showed recurrent amplification in liposarcomas.

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Architecture of High Mobility Group Protein I-C·DNA Complex and Its Perturbation upon Phosphorylation by Cdc2 Kinase

Cited by 38 publications

References 52 publications

Spatial Contacts and Nucleosome Step Movements Induced by the NURF Chromatin Remodeling Complex

Spatial Contacts and Nucleosome Step Movements Induced by the NURF Chromatin Remodeling Complex

Distinct Organization of DNA Complexes of Various HMGI/Y Family Proteins and Their Modulation upon Mitotic Phosphorylation

Ectopic sequences from truncated HMGIC in liposarcomas are derived from various amplified chromosomal regions

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