Specificity of Mammalian Y-box Binding Protein p50 in Interaction with ss and ds DNA Analyzed with Generic Oligonucleotide Microchip

Zasedateleva, Olga A.; Крылов, А. С.; Prokopenko, Dmitry; Skabkin, Maxim A.; Ovchinnikov, Lev P.; Kolchinsky, Alexander; Mirzabekov, Andrei D.

doi:10.1016/s0022-2836(02)00937-3

Cited by 51 publications

(49 citation statements)

References 49 publications

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“…3). rp 3/4 contains the motif GGTG/CACC, and rp 6/7 contains the motif GATG/CATC, which are efficiently recognized by Y-box proteins (Zasedateleva et al, 2002). Although the lengths of the rp 3/4 and rp 6/7 oligonucleotides are similar, the complexes produced by these oligonucleotides in EMSA with the YB-1 protein differ (Fig.…”

Section: Discussionmentioning

confidence: 95%

“…This phenomenon may be explained by the differences in the primary nucleotide sequence of the YB-1 recognition sequence, which may determine the binding characteristics of YB-1 (Spitkovsky et al, 1992). It is now generally accepted that YB-1 functions are, in part, dependent on the DNA secondary structure (Swamynathan et al, 1998;Zasedateleva et al, 2002). It is therefore plausible that a particular composition of the individual repeats in Stin2 VNTR may result in different structural conformation of this regulatory region, thus leading to combinatorial functional outcome.…”

Section: Discussionmentioning

confidence: 99%

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YB-1 and CTCF Differentially Regulate the 5-HTT Polymorphic Intron 2 Enhancer Which Predisposes to a Variety of Neurological Disorders

Klenova¹,

Scott²,

Roberts³

et al. 2004

J. Neurosci.

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Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

YB-1 and CTCF Differentially Regulate the 5-HTT Polymorphic Intron 2 Enhancer Which Predisposes to a Variety of Neurological Disorders

Klenova¹,

Scott²,

Roberts³

et al. 2004

J. Neurosci.

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“…71 With SELEX and Chip methods, it was established that the strings of nucleic acids preferred by YB-1 are GGGG (ssDNA), CACC/T (double-stranded DNA (dsDNA)) and AACAUC (RNA). None of these motifs resemble to a canonical Y/CCAAT box (Bouvet et al, 72 Zasedateleva et al 73 and Ray et al 74 ; reviewed by Eliseeva et al 71 ). In vitro, YB-1 prefers RNA and ssDNA -K D in the order of 10 À 9 -with respect to dsDNA.…”

Section: Nf-y Is the Sequence-specific Ccaat Factormentioning

confidence: 99%

Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y?

Dolfini

Mantovani

2013

Cell Death Differ

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The Y box is an important sequence motif found in promoters and enhancers containing a CCAAT box -one of the few elements enriched in promoters of large sets of genes overexpressed in cancer. The search for the transcription factor(s) acting on it led to the biochemical purification of the nuclear factor Y (NF-Y) heterotrimer, and to the cloning -through the screening of expression libraries -of Y box-binding protein 1 (YB-1), an oncogene, overexpressed in aggressive tumors and associated with drug resistance. These two factors have been associated with Y/CCAAT-dependent activation of numerous growth-related genes, notably multidrug resistance protein 1. We review two decades of data indicating that NF-Y ultimately acts on Y/CCAAT in cancer cells, a notion recently confirmed by genome-wide data. Other features of YB-1, such as post-transcriptional control of mRNA biology, render it important in cancer biology.

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“…Coles et al (2005) demonstrated that binding of YB1 to the vascular endothelial growth factor promoter prevented the binding of other transcription factors and resulted in the inhibition of transcription and translation. It has also been shown that YB1 binding to the ssDNA region of a promoter resulted in the stabilization of ssDNA that also inhibited gene transcription and translation (Zasedateleva et al, 2002;Dooley et al, 2006). Therefore, it is possible that down-regulation of YB1 promoted E2A binding to the AAV2p5 promoter that synergistically contributed to the significant increase in AAV Rep gene expression and vector titers observed in this study.…”

Section: Discussionmentioning

confidence: 56%

“…YB1 packs and stabilizes mRNA to mediate gene regulation at different levels (Eliseeva et al, 2011). YB1 has a far higher affinity for a single-stranded DNA (ssDNA) than doublestranded DNA (Hasegawa et al, 1991;MacDonald et al, 1995;Izumi et al, 2001;Coles et al, 2005) and has the greatest binding preference for the single-stranded DNA motif GGGG(TT) (Zasedateleva et al, 2002). Analysis of the single-stranded AAV2 DNA genome showed that such a single-stranded GGGG(TT) motif is presented within the AAV2 ITR region from nucleotide 137 to 142 of the AAV2 genome (NCBI sequence NC_001401.2), indicating a potential AAV DNA binding site for the YB1 protein.…”

Section: Discussionmentioning

confidence: 99%

Establishment of a Novel Cell Line for the Enhanced Production of Recombinant Adeno-Associated Virus Vectors for Gene Therapy

et al. 2014

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Adeno-associated viral (AAV) vectors show great promise because of their excellent safety profile; however, preexisting immune responses have necessitated the administration of high titer AAV, posing a significant challenge to the advancement of gene therapy involving AAV vectors. Recombinant AAV vectors contain minimum viral proteins necessary for their assembly and gene delivery functions. During the process of AAV assembly and production, AAV vectors acquire, inherently and submissively, various cellular proteins, but the identity of these proteins is poorly characterized. We reason that by identifying host cell proteins inherently associated with AAV vectors we may better understand the contribution of cellular components to AAV vector assembly and, ultimately, may improve the production of AAV vectors for gene therapy. In this study, three serotypes of recombinant AAV, namely AAV2, AAV5, and AAV8, were investigated. We used liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) methods to identify protein composition in purified AAV vectors, confirmed protein identities using western blotting, and explored the potential function of selected proteins in AAV vector production using small hairpin (shRNA) methods. Using LC-MS/MS, we identified 44 AAVassociated cellular proteins including Y-box binding protein (YB1). We showed for the first time that the establishment of a novel producer cell line by introducing an shRNA sequence down-regulating YB1 resulted in up to 45-and 9-fold increase in physical vector genome titers of AAV2 and AAV8, respectively, and up to 7-fold increase in AAV2 transduction vector genome titers. Our results revealed that YB1 gene knockdown promoted AAV2 rep expression and vector DNA production and reduced the number of empty particles in AAV2 products, suggesting that YB1 plays an important role in AAV vector assembly by competition with adenovirus E2A and AAV capsid proteins for binding to the inverted terminal repeat (ITR) sequence. The significance and implications of our findings in future improvement of AAV production are discussed.

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Specificity of Mammalian Y-box Binding Protein p50 in Interaction with ss and ds DNA Analyzed with Generic Oligonucleotide Microchip

Cited by 51 publications

References 49 publications

YB-1 and CTCF Differentially Regulate the 5-HTT Polymorphic Intron 2 Enhancer Which Predisposes to a Variety of Neurological Disorders

YB-1 and CTCF Differentially Regulate the 5-HTT Polymorphic Intron 2 Enhancer Which Predisposes to a Variety of Neurological Disorders

Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y?

Establishment of a Novel Cell Line for the Enhanced Production of Recombinant Adeno-Associated Virus Vectors for Gene Therapy

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