scholarly journals Tumorigenesis by Meis1 overexpression is accompanied by a change of DNA target-sequence specificity which allows binding to the AP-1 element

Oncotarget ◽  
2015 ◽  
Vol 6 (28) ◽  
pp. 25175-25187 ◽  
Author(s):  
Leila Dardaei ◽  
Dmitry Penkov ◽  
Lisa Mathiasen ◽  
Pranami Bora ◽  
Marco J. Morelli ◽  
...  
Keyword(s):  
Target Sequence ◽  
Sequence Specificity

scholarly journals Benchmarking substrate-based kinase activity inference using phosphoproteomic data

2016 ◽  
Author(s):  
Claudia Hernandez-Armenta ◽  
David Ochoa ◽  
Emanuel Gonçalves ◽  
Julio Saez-Rodriguez ◽  
Pedro Beltrao
Keyword(s):  
Kinase Activity ◽  
Multiple Linear Regression Model ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Gold Standard Dataset ◽  
Kolmogorov Smirnov

AbstractMotivationPhosphoproteomic experiments are increasingly used to study the changes in signalling occurring across different conditions. It has been proposed that changes in phosphorylation of kinase target sites can be used to infer when a kinase activity is under regulation. However, these approaches have not yet been benchmarked due to a lack of appropriate benchmarking strategies.ResultsWe curated public phosphoproteomic experiments to identify a gold standard dataset containing a total of 184 kinase-condition pairs where regulation is expected to occur. A list of kinase substrates was compiled and used to estimate changes in kinase activities using the following methods: Z-test, Kolmogorov Smirnov test, Wilcoxon rank sum test, gene set enrichment analysis (GSEA), and a multiple linear regression model (MLR). We also tested weighted variants of the Z-test, and GSEA that include information on kinase sequence specificity as proxy for affinity. Finally, we tested how the number of known substrates and the type of evidence (in vivo, in vitro or in silico) supporting these influence the predictions.ConclusionsMost models performed well with the Z-test and the GSEA performing best as determined by the area under the ROc curve (Mean AUC=0.722). Weighting kinase targets by the kinase target sequence preference improves the results only marginally. However, the number of known substrates and the evidence supporting the interactions has a strong effect on the predictions.

Host-induced gene silencing and spray-induced gene silencing for crop protection against viruses.

2021 ◽  
pp. 72-85
Author(s):  
Angela Ricci ◽  
Silvia Sabbadini ◽  
Laura Miozzi ◽  
Bruno Mezzetti ◽  
Emanuela Noris
Keyword(s):  
Gene Silencing ◽  
Plant Pathogens ◽  
Crop Protection ◽  
Plant Defence ◽  
Transcriptional Gene Silencing ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Rna Molecules ◽  
Political Concern ◽  
Post Transcriptional Gene Silencing

Abstract Since the beginning of agriculture, plant virus diseases have been a strong challenge for farming. Following its discovery at the very beginning of the 1990s, the RNA interference (RNAi) mechanism has been widely studied and exploited as an integrative tool to obtain resistance to viruses in several plant species, with high target-sequence specificity. In this chapter, we describe and review the major aspects of host-induced gene silencing (HIGS), as one of the possible plant defence methods, using genetic engineering techniques. In particular, we focus our attention on the use of RNAi-based gene constructs to introduce stable resistance in host plants against viral diseases, by triggering post-transcriptional gene silencing (PTGS). Recently, spray-induced gene silencing (SIGS), consisting of the topical application of small RNA molecules to plants, has been explored as an alternative tool to the stable integration of RNAi-based gene constructs in plants. SIGS has great and innovative potential for crop defence against different plant pathogens and pests and is expected to raise less public and political concern, as it does not alter the genetic structure of the plant.

scholarly journals Sequence specificity in DNA binding is determined by association rather than dissociation

2021 ◽  
Author(s):  
Emil Marklund ◽  
Guanzhong Mao ◽  
Sebastian Deindl ◽  
Johan Elf
Keyword(s):  
Dna Binding ◽  
Genetic Information ◽  
Specific Binding ◽  
Theoretical Framework ◽  
Simple Equation ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Target Search ◽  
Target Binding ◽  
Site Recognition

AbstractSequence-specific binding of proteins to DNA is essential for accessing genetic information. Here, we derive a simple equation for target-site recognition, which uncovers a previously unrecognized coupling between the macroscopic association and dissociation rates of the searching protein. Importantly, this relationship makes it possible to recover the relevant microscopic rates from experimentally determined macroscopic ones. We directly test the equation by observing the binding and unbinding of individual lac repressor (LacI) molecules during target search. We find that LacI dissociates from different target sequences with essentially identical microscopic dissociation rates. Instead, sequence specificity is determined by the efficiency with which the protein recognizes different targets, effectively reducing its risk of being retained on a non-target sequence. Our theoretical framework also accounts for the coupling between off-target binding and unbinding of the catalytically inactive Cas9 (dCas9), showing that the binding pathway can be obtained from macroscopic data.One Sentence SummaryAssociation and dissociation rates are anti-correlated for reactions that include a nonspecific probing step.

scholarly journals An Improved Transposon for the Halophilic ArchaeonHaloarcula hispanica

1999 ◽  
Vol 181 (22) ◽  
pp. 7140-7142 ◽  
Author(s):  
Wayne G. Woods ◽  
Katrina Ngui ◽  
Michael L. Dyall-Smith
Keyword(s):  
Insertion Sequence ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Haloarcula Hispanica

ABSTRACT An improved transposon (ThD73) for Haloarcula hispanica is described. Based on the halobacterial insertion sequence ISH28, it showed little target sequence specificity but was biased toward a lower G+C content. Twenty randomly selected ThD73 mutants were analyzed, and the DNA flanking their insertions revealed several recognizable sequences, including two (unrelated) ISH elements.

Sequence Specificity in the Higher-Order Interaction of the Rev Protein of HIV-1 with its Target Sequence, the RRE

1995 ◽  
Vol 10 (3) ◽  
pp. 317???323 ◽  
Author(s):  
Douglas M. Powell ◽  
Ming Jie Zhang ◽  
Danielle A. M. Konings ◽  
Paul T. Wingfield ◽  
Stephen J. Stahl ◽  
...  
Keyword(s):  
Higher Order ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Order Interaction ◽  
Hiv 1 ◽  
Rev Protein

MyoD and myogenin act on the chicken myosin light-chain 1 gene as distinct transcriptional factors

1993 ◽  
Vol 13 (11) ◽  
pp. 7153-7162
Author(s):  
A Asakura ◽  
A Fujisawa-Sehara ◽  
T Komiya ◽  
Y Nabeshima ◽  
Y Nabeshima
Keyword(s):  
Light Chain ◽  
Dna Sequences ◽  
Regulatory Region ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Nonmuscle Cells ◽  
Flanking Sequences ◽  
E Boxes

Expression of MyoD, myogenin, MRF4, and Myf-5 converts nonmuscle cells to muscle cells. In an attempt to analyze the roles of these factors, we have investigated their effects on transcription driven by the promoter of the chicken myosin alkaline light-chain (MLC1) gene. The activation by CMD1 or c-myogenin (chicken MyoD or myogenin, respectively) was dependent on the existence of a muscle-specific regulatory region located from positions -2096 to -1743. Its distal half, containing a pair of E boxes (CANNTG), had been previously characterized as an enhancer responsive to CMD1 but not to c-myogenin. In this study, we report the identification of another enhancer in the muscle-specific regulatory region which is preferentially responsive to c-myogenin. Deletion and mutation analyses indicated that this enhancer requires a single E box and its flanking sequences. Furthermore, analysis of chimeric proteins of CMD1 and c-myogenin indicated that regions outside the basic helix-loop-helix domain of c-myogenin are involved in the specificity of the enhancer. These results show that CMD1 and c-myogenin act on the MLC1 gene by recognizing different upstream DNA sequences and that direct or indirect interactions between the regions outside the basic helix-loop-helix domain and flanking sequences of E boxes are involved in the target sequence specificity.

Extended Target Sequence Specificity of PNA-Minor-Groove Binder Conjugates

ChemBioChem ◽  
2004 ◽  
Vol 6 (1) ◽  
pp. 66-68 ◽  
Author(s):  
Peter E. Nielsen ◽  
Karin Frederiksen ◽  
Carsten Behrens
Keyword(s):  
Minor Groove ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Minor Groove Binder ◽  
Extended Target

scholarly journals MyoD and myogenin act on the chicken myosin light-chain 1 gene as distinct transcriptional factors.

1993 ◽  
Vol 13 (11) ◽  
pp. 7153-7162 ◽  
Author(s):  
A Asakura ◽  
A Fujisawa-Sehara ◽  
T Komiya ◽  
Y Nabeshima ◽  
Y Nabeshima
Keyword(s):  
Light Chain ◽  
Dna Sequences ◽  
Regulatory Region ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Nonmuscle Cells ◽  
Flanking Sequences ◽  
E Boxes

Expression of MyoD, myogenin, MRF4, and Myf-5 converts nonmuscle cells to muscle cells. In an attempt to analyze the roles of these factors, we have investigated their effects on transcription driven by the promoter of the chicken myosin alkaline light-chain (MLC1) gene. The activation by CMD1 or c-myogenin (chicken MyoD or myogenin, respectively) was dependent on the existence of a muscle-specific regulatory region located from positions -2096 to -1743. Its distal half, containing a pair of E boxes (CANNTG), had been previously characterized as an enhancer responsive to CMD1 but not to c-myogenin. In this study, we report the identification of another enhancer in the muscle-specific regulatory region which is preferentially responsive to c-myogenin. Deletion and mutation analyses indicated that this enhancer requires a single E box and its flanking sequences. Furthermore, analysis of chimeric proteins of CMD1 and c-myogenin indicated that regions outside the basic helix-loop-helix domain of c-myogenin are involved in the specificity of the enhancer. These results show that CMD1 and c-myogenin act on the MLC1 gene by recognizing different upstream DNA sequences and that direct or indirect interactions between the regions outside the basic helix-loop-helix domain and flanking sequences of E boxes are involved in the target sequence specificity.

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