Human Ku Antigen Tightly Binds and Stabilizes a Tetrahelical Form of the Fragile X Syndrome d(CGG)  Expanded Sequence

Uliel, Livnat; Weisman-Shomer, Pnina; Oren-Jazan, Hely; Newcomb, Terry; Loeb, Lawrence A.; Fry, Michael

doi:10.1074/jbc.m005542200

Cited by 26 publications

(16 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Ku proteins have the capacity to interact with circular DNA with bubbles and any structure containing a double-to-single strand transition (64). In vitro data indicate that Ku70 binds to and stabilize the tetrahelical form of the Fragile X syndrome d(CGG) n expanded sequence (65). However, the protein associated with NHE, which is particularly interesting in the context of KRAS transcription is hnRNP A1, as its N-terminus proteolitic portion (residues 1–195), referred to UP1, shows the ability to resolve G4-DNA.…”

Section: Discussionmentioning

confidence: 99%

Structural polymorphism within a regulatory element of the human KRAS promoter: formation of G4-DNA recognized by nuclear proteins

Cogoi

Paramasivam

Spolaore

et al. 2008

Nucleic Acids Research

149

168

View full text Add to dashboard Cite

The human KRAS proto-oncogene contains a critical nuclease hypersensitive element (NHE) upstream of the major transcription initiation site. In this article, we demonstrate by primer-extension experiments, PAGE, chemical footprinting, CD, UV and FRET experiments that the G-rich strand of NHE (32R) folds into intra-molecular G-quadruplex structures. Fluorescence data show that 32R in 100 mM KCl melts with a biphasic profile, showing the formation of two distinct G-quadruplexes with Tm of ∼55°C (Q1) and ∼72°C (Q2). DMS-footprinting and CD suggest that Q1 can be a parallel and Q2 a mixed parallel/antiparallel G-quadruplex. When dsNHE (32R hybridized to its complementary) is incubated with a nuclear extract from Panc-1 cells, three DNA–protein complexes are observed by EMSA. The complex of slower mobility is competed by quadruplex 32R, but not by mutant oligonucleotides, which cannot form a quadruplex structure. Using paramagnetic beads coupled with 32R, we pulled down from the Panc-1 extract proteins with affinity for quadruplex 32R. One of these is the heterogeneous nuclear ribonucleoprotein A1, which was previously reported to unfold quadruplex DNA. Our study suggests a role of quadruplex DNA in KRAS transcription and provides the basis for the rationale design of molecular strategies to inhibit the expression of KRAS.

show abstract

Section: Discussionmentioning

confidence: 99%

Structural polymorphism within a regulatory element of the human KRAS promoter: formation of G4-DNA recognized by nuclear proteins

Cogoi

Paramasivam

Spolaore

et al. 2008

Nucleic Acids Research

149

168

View full text Add to dashboard Cite

show abstract

“…Many proteins have been reported to bind to quadruplex DNA and some of them, including the Ku antigen, demonstrated an ability to stabilize the quadruplex structure (36). In addition, only some proteins, such as BLM helicase, WRN helicase, and murine telomeric DNA binding proteins, qTBP42 and uqTBP25, were reported to unwind tetra-or bi-molecular quadruplex DNA (37)(38)(39).…”

Section: Discussionmentioning

confidence: 99%

Unfolding of quadruplex structure in the G-rich strand of the minisatellite repeat by the binding protein UP1

Fukuda

Katahira

Tsuchiya

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

107

102

View full text Add to dashboard Cite

The mouse hypervariable minisatellite (MN) Pc-1 consists of tandem repeats of d(GGCAG) and flanked sequences. We have previously demonstrated that single-stranded d(GGCAG)n folds into the intramolecular folded-back quadruplex structure under physiological conditions. Because DNA polymerase progression in vitro is blocked at the repeat, the characteristic intramolecular quadruplex structure of the repeat, at least in part, could be responsible M inisatellites (MNs), also called variable number of tandem repeats, are arrays of 5-to 100-bp repeats widely dispersed in eukaryotic genomes (1). Some have been suggested to be implicated in genetic predisposition to various human diseases. Although MNs are known to be hot spots for meiotic recombination in germ cells (1, 2), they are considered to be genetically stable in somatic cells (3). However, they also have been demonstrated to be altered in somatic cells with exposure to chemical carcinogens, ␥ irradiation, or UV irradiation (4-7). They also exhibit alterations in a range of tumors of humans and experimental animals (8-10).The MN Pc-1, located on mouse chromosome 4, consists of tandem repeats of d(GGCAG) (11, 12). The germ-line mutation rate for Pc-1 is 15% per gamete, whereas the mutation rate in somatic cells is 2-3% per 22-24 population doublings (12-14). Many hypervariable MNs, consisting of G-rich repeat units similar to Pc-1, have been found in the mouse and other mammalian genomes, and mouse MNs containing d(GGCAG) n or d(GGCAGG) n motifs are very unstable in germ-line cells (11). Pc-1 and Pc-1-like MNs were demonstrated to be strikingly unstable by DNA fingerprint analysis, both in fibroblasts deficient in DNA-dependent protein kinase activity and in NIH 3T3 cells treated with okadaic acid, an inhibitor of protein phosphatases (13,14).Although the molecular mechanisms underlying the induction of MN mutations are largely unknown, the G-rich strand of Pc-1 is known to form an intramolecular folded-back quadruplex structure under physiological conditions and cause arrest of DNA synthesis (15). We have isolated six MN Pc-1 binding proteins (MNBPs) from NIH 3T3 cells (16). Two of them, MNBP-A and MNBP-B, bind to the G-rich strand of Pc-1, and the other four, MNBP-D, MNBP-E, MNBP-F, and MNBP-G, to the complementary C-rich strand.In this article, we document isolation of cDNA clones encoding MNBP-B and characterization of a recombinant MNBP-B. Sequences of seven proteolytic peptides of purified MNBP-B were determined, and cDNA clones were subsequently isolated. MNBP-B was revealed to be identical to the single-stranded DNA binding protein, UP1 (17), which is a proteolytic product corresponding to the N-terminal 195 aa of the 34-kDa heterogeneous nuclear ribonucleoprotein (hnRNP) A1 (18, 19). DNA binding specificity and in vitro effect on quadruplex structures of UP1 were analyzed to cast light on its biological roles. EMSA. EMSA and analyses of oligonucleotide competition using EMSA were performed as detailed (16) with 32 P-labeled pG8 (final concentration 2 nM)...

show abstract

“…Although there is as yet no physical or genetic evidence for these structures in vivo, several observations suggest they might form. First, human proteins such as WRN helicase, human Ku and telomeric tetraplex DNA binding proteins qTBP42 and uqTBP25 preferentially recognize and modulate the stability of CGG quadruplex structures in vitro (Fry and Loeb, 1999;Uliel et al, 2000;WeismanShomer et al, 2000b). Second, the CGG quadruplex structures act as a block to DNA synthesis in vitro (Usdin and Woodford, 1995;Usdin, 1998;Kamath-Loeb et al, 2001).…”

Section: Structural Features Of Trinucleotide Repeat Dnamentioning

confidence: 99%

Trinucleotide repeat instability: a hairpin curve at the crossroads of replication, recombination, and repair

Lenzmeier

Freudenreich

2003

Cytogenet Genome Res

View full text Add to dashboard Cite

The trinucleotide repeats that expand to cause human disease form hairpin structures in vitro that are proposed to be the major source of their genetic instability in vivo. If a replication fork is a train speeding along a track of double-stranded DNA, the trinucleotide repeats are a hairpin curve in the track. Experiments have demonstrated that the train can become derailed at the hairpin curve, resulting in significant damage to the track. Repair of the track often results in contractions and expansions of track length. In this review we introduce the in vitro evidence for why CTG/CAG and CCG/CGG repeats are inherently unstable and discuss how experiments in model organisms have implicated the replication, recombination and repair machinery as contributors to trinucleotide repeat instability in vivo.

show abstract

Human Ku Antigen Tightly Binds and Stabilizes a Tetrahelical Form of the Fragile X Syndrome d(CGG) Expanded Sequence

Abstract: Hairpin and tetrahelical structures of a d(CGG)n

Cited by 26 publications

References 59 publications

Structural polymorphism within a regulatory element of the human KRAS promoter: formation of G4-DNA recognized by nuclear proteins

Structural polymorphism within a regulatory element of the human KRAS promoter: formation of G4-DNA recognized by nuclear proteins

Unfolding of quadruplex structure in the G-rich strand of the minisatellite repeat by the binding protein UP1

Trinucleotide repeat instability: a hairpin curve at the crossroads of replication, recombination, and repair

Contact Info

Product

Resources

About