Correlations between Scaffold/Matrix Attachment Region (S/MAR) Binding Activity and DNA Duplex Destabilization Energy

Bode, Jürgen; Winkelmann, Silke; Götze, Sandra; Spiker, Steven; Tsutsui, Ken; Bi, Chengpeng; Prashanth, A K; Benham, Craig J.

doi:10.1016/j.jmb.2005.11.073

Cited by 55 publications

(56 citation statements)

References 89 publications

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“…the presence of a BUR. 16 Most important in the present context are observations that PARP-1, by binding to BUR-related structures in its promoter, down-regulates its own expression. 5,17 According to our model, 3 this process may involve the PARP-1-mediated translocation of its own gene into a silencing nuclear compartment (see below).…”

Section: Introductionmentioning

confidence: 84%

PARP-1 Expression in the Mouse is Controlled by an Autoregulatory Loop: PARP-1 Binding to an Upstream S/MAR Element and to a Novel Recognition Motif in its Promoter Suppresses Transcription

Vidaković

Gluch

Jian

et al. 2009

Journal of Molecular Biology

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Section: Introductionmentioning

confidence: 84%

PARP-1 Expression in the Mouse is Controlled by an Autoregulatory Loop: PARP-1 Binding to an Upstream S/MAR Element and to a Novel Recognition Motif in its Promoter Suppresses Transcription

Vidaković

Gluch

Jian

et al. 2009

Journal of Molecular Biology

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“…Research has indicated that chromosomal sites that are susceptible to superhelical strand separation are required in both prokaryotes and eukaryotes for the initiation of DNA replication. In some instances an SIDD region is sufficient to initiate these processes without the help of DNA-binding proteins Bode et al, 2006). Usually, the least stable regions tend to be A-T rich, but whether a transition occurs at a given site depends not just on the local sequence properties but also on how the site competes with all the others in the domain .…”

Section: Putative Origins Of Replicationmentioning

confidence: 99%

Long-Term Episomal Transgene Expression from Mitotically Stable Integration-Deficient Lentiviral Vectors

et al. 2014

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Nonintegrating gene delivery vectors have an improved safety profile compared with integrating vectors, but transgene retention is problematic as nonreplicating episomes are progressively and rapidly diluted out through cell division. We have developed an integration-deficient lentiviral vector (IDLV) system generating mitotically stable episomes capable of long-term transgene expression. We found that a transient cell cycle arrest at the time of transduction with IDLVs resulted in 13-45% of Chinese hamster ovary (CHO) cells expressing the transgene for over 100 cell generations in the absence of selection. The use of a scaffold/matrix attachment region did not result in improved episomal retention in this system, and episomes did not form after transduction with adeno-associated viral or minicircle vectors under the same conditions. Investigations into the episomal status of the vector genome using (1) linear amplification-mediated polymerase chain reaction followed by deep sequencing of vector-genome junctions, (2) Southern blotting, and (3) fluorescent in situ hybridization strongly suggest that the vector is not integrated in the vast majority of cells. In conclusion, we have developed an IDLV procedure generating mitotically stable episomes capable of long-term transgene expression. The application of this approach to stem cell populations could significantly improve the safety profile of a range of stem and progenitor cell gene therapies.

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“…Among the members of the hnRNA family of proteins, the hnRNP Q plays an important role in regulating alternative pre-mRNA splicing (Shyu and Wilkinson 2000;Chen et al 2008). Scaffold associated regions (SAR, also termed matrix associated regions, MAR) are DNA sequence elements that mediates specific binding to the nuclear scaffold, forming a base of DNA loops in an eukaryotic cell (Bode et al 2005;Sun et al 2006).…”

Section: Expression Stability Of the Candidate Internal Control Genesmentioning

confidence: 99%

Genome-wide identification and evaluation of novel internal control genes for Q-PCR based transcript normalization in wheat

et al. 2010

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To accurately quantify gene expression using quantitative PCR amplification, it is vital that one or more ideal internal control genes are used to normalize the samples to be compared. Ideally, the expression level of those internal control genes should vary as little as possible between tissues, developmental stages and environmental conditions. In this study, 32 candidate genes for internal control were obtained from the analysis of nine independent experiments which included 333 Affymetrix GeneChip Wheat Genome arrays. Expression levels of the selected genes were then evaluated by quantitative real-time PCR with cDNA samples from different tissues, stages of development and environmental conditions. Finally, fifteen novel internal control genes were selected and their respective expression profiles were compared using NormFinder, geNorm, Pearson correlation coefficients and the twofold-change method. The novel internal control genes from this study were compared with thirteen traditional ones for their expression stability. It was observed that seven of the novel internal control genes were better than the traditional ones in expression stability under all the tested cDNA samples. Among the traditional internal control genes, the elongation factor 1-alpha exhibited strong expression stability, whereas the 18S rRNA, Alpha-tubulin, Actin and GAPDH genes had very poor expression stability in the range of wheat samples tested. Therefore, the use of the novel internal control genes for normalization should improve the accuracy and validity of gene expression analysis.

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Correlations between Scaffold/Matrix Attachment Region (S/MAR) Binding Activity and DNA Duplex Destabilization Energy

Cited by 55 publications

References 89 publications

PARP-1 Expression in the Mouse is Controlled by an Autoregulatory Loop: PARP-1 Binding to an Upstream S/MAR Element and to a Novel Recognition Motif in its Promoter Suppresses Transcription

PARP-1 Expression in the Mouse is Controlled by an Autoregulatory Loop: PARP-1 Binding to an Upstream S/MAR Element and to a Novel Recognition Motif in its Promoter Suppresses Transcription

Long-Term Episomal Transgene Expression from Mitotically Stable Integration-Deficient Lentiviral Vectors

Genome-wide identification and evaluation of novel internal control genes for Q-PCR based transcript normalization in wheat

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