scholarly journals Analyzing and Tuning Ribozyme Activity by Deep Sequencing To Modulate Gene Expression Level in Mammalian Cells

2018 ◽  
Vol 7 (2) ◽  
pp. 371-376 ◽  
Author(s):  
Shungo Kobori ◽  
Yohei Yokobayashi
Keyword(s):  
Gene Expression ◽  
Deep Sequencing ◽  
Mammalian Cells ◽  
Gene Expression Level ◽  
Expression Level

scholarly journals Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Georg Back ◽  
Dirk Walther
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Deep Sequencing ◽  
Gene Expression Level ◽  
Expression Level ◽  
Regulatory Role ◽  
Sequence Motifs ◽  
Related Sequence ◽  
Genomic Features ◽  
Wide Range

Abstract Background Intron mediated enhancement (IME) is the potential of introns to enhance the expression of its respective gene. This essential function of introns has been observed in a wide range of species, including fungi, plants, and animals. However, the mechanisms underlying the enhancement are as of yet poorly understood. The goal of this study was to identify potential IME-related sequence motifs and genomic features in first introns of genes in Arabidopsis thaliana. Results Based on the rationale that functional sequence motifs are evolutionarily conserved, we exploited the deep sequencing information available for Arabidopsis thaliana, covering more than one thousand Arabidopsis accessions, and identified 81 candidate hexamer motifs with increased conservation across all accessions that also exhibit positional occurrence preferences. Of those, 71 were found associated with increased correlation of gene expression of genes harboring them, suggesting a cis-regulatory role. Filtering further for effect on gene expression correlation yielded a set of 16 hexamer motifs, corresponding to five consensus motifs. While all five motifs represent new motif definitions, two are similar to the two previously reported IME-motifs, whereas three are altogether novel. Both consensus and hexamer motifs were found associated with higher expression of alleles harboring them as compared to alleles containing mutated motif variants as found in naturally occurring Arabidopsis accessions. To identify additional IME-related genomic features, Random Forest models were trained for the classification of gene expression level based on an array of sequence-related features. The results indicate that introns contain information with regard to gene expression level and suggest sequence-compositional features as most informative, while position-related features, thought to be of central importance before, were found with lower than expected relevance. Conclusions Exploiting deep sequencing and broad gene expression information and on a genome-wide scale, this study confirmed the regulatory role on first-introns, characterized their intra-species conservation, and identified a set of novel sequence motifs located in first introns of genes in the genome of the plant Arabidopsis thaliana that may play a role in inducing high and correlated gene expression of the genes harboring them.

scholarly journals Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in the plant Arabidopsis thaliana

2021 ◽  
Author(s):  
Georg Back ◽  
Dirk Walther
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Deep Sequencing ◽  
Gene Expression Level ◽  
Expression Level ◽  
Regulatory Role ◽  
Sequence Motifs ◽  
Genomic Features ◽  
Wide Range ◽  
Plant Arabidopsis Thaliana

Abstract Background. Intron mediated enhancement (IME) is the potential of introns to enhance expression of its respective gene. This essential function of introns has been observed in a wide range of species, including fungi, plants, and animals. Studies in the plant ​ Arabidopsis thaliana have shown that enhancing introns exhibit a distinct base composition and are generally the first intron located close to the transcription start site. However, the mechanisms underlying the enhancement are as of yet poorly understood. The goal of the study was to identify potential IME-related sequence motifs and genomic features found in first introns of genes in the plant Arabidopsis thaliana. Results. Based on the rationale that functionale sequence motifs are evolutionarily conserved, we exploited the deep sequencing information available for Arabidopsis thaliana, covering more than one thousand Arabidopsis accessions, and identified 81 candidate hexamer motifs with increased conservation across all accessions, and which also exhibited positional occurrence preferences. Of those, 71 were found associated with increased correlation of gene expression of genes harboring them, suggesting a cis-regulatory role. Filtering further for effect on gene expression correlation yielded a set of 16 hexamer motifs, corresponding to five consensus motifs. While all five motifs represent new motif definitions, two are similar to the two previously reported IME-motifs, whereas three are altogether novel. To identify additional IME-related genomic features, Random Forest models were trained for classification of gene expression level based on an array of different sequence-related features. The results indicate that introns harbor information with regard to gene expression level and suggest sequence-compositional features as most informative, while position-related features, that were thought to be of central importance before, were found with lower than expected relevance. Conclusions. ​ Exploiting deep sequencing and broad gene expression information and on a genome-wide scale, this study confirmed the regulatory role on first-introns, characterized their intra-species conservation, and identified a set of novel sequence motifs located in first introns of genes in the genome of the plant ​ Arabidopsis thalian​ a that may play a role in inducing high and correlated gene expression of the genes harboring them.

Gene Expression Level Analysis

2020 ◽  
Author(s):  
Keyword(s):  
Gene Expression ◽  
Gene Expression Level ◽  
Expression Level ◽  
Level Analysis

scholarly journals Effect of specific production rate of recombinant protein on multimerization of plasmid vector and gene expression level

1999 ◽  
Vol 179 (2) ◽  
pp. 367-373 ◽  
Author(s):  
Vibhor Saraswat ◽  
Dae Young Kim ◽  
Jeewon Lee ◽  
Young-Hoon Park
Keyword(s):  
Gene Expression ◽  
Recombinant Protein ◽  
Production Rate ◽  
Plasmid Vector ◽  
Gene Expression Level ◽  
Expression Level ◽  
Specific Production ◽  
Specific Production Rate

The investigation of CD36 scavenger receptor and MSR1 scavenger receptor gene expression level in patients with atherosclerosis

2010 ◽  
Vol 27 ◽  
pp. S66
Author(s):  
M. Piechota ◽  
A. Banaszewska ◽  
E. Guzniczak ◽  
G. Rosinski ◽  
T. Siminiak ◽  
...  
Keyword(s):  
Gene Expression ◽  
Receptor Gene ◽  
Scavenger Receptor ◽  
Gene Expression Level ◽  
Expression Level ◽  
Receptor Gene Expression

SAT0005 Human C-Type Lectin Domain Family 4, Member C Gene Expression Level Helps Predict Future Clinical Response to Tabalumab Blockade of Baff in Rheumatoid Arthritis

2013 ◽  
Vol 72 (Suppl 3) ◽  
pp. A580.2-A580
Author(s):  
E. R. Dow ◽  
P. Banerjee ◽  
M. A. Penny ◽  
E. Nantz ◽  
S. Stepaniants ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Clinical Response ◽  
Gene Expression Level ◽  
Expression Level ◽  
Domain Family ◽  
Lectin Domain

The impact of gene-body H3K36me3 patterns on gene expression level changes in chronic myelogenous leukemia

Gene ◽  
2021 ◽  
pp. 145862
Author(s):  
Lu-Qiang Zhang ◽  
Jun-Jie Liu ◽  
Li Liu ◽  
Guo-Liang Fan ◽  
Yan-Nan Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Myelogenous Leukemia ◽  
Myelogenous Leukemia ◽  
Gene Expression Level ◽  
Expression Level ◽  
Gene Body ◽  
The Impact

scholarly journals Elevated Lipocalin-2 Can Indicate the Vascular Inflammation in Patients with Ischemic Stroke

2019 ◽  
Author(s):  
Rajnics P ◽  
◽  
Kellner A ◽  
Nagy F ◽  
Alföldi V ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ischemic Stroke ◽  
Gene Expression Level ◽  
Expression Level ◽  
Neutrophil Granulocytes ◽  
Lipocalin 2 ◽  
Relative Gene Expression ◽  
Thrombotic Risk ◽  
Relative Gene ◽  
Relative Gene Expression Level

Purpose: Elevated level of Lipocalin-2 (LCN2), a new acute phase adipokine, was described after ischemic stroke. A number of researchers feel as though that LCN2 originated from the infiltrating neutrophils and other cells in brain after stroke. Others measured elevated LCN2 expression in arteriosclerotic plaque. Therefore we have investigated LCN2 relative gene expression level of blood neutrophil granulocytes in patients with ischemic stroke to assess if elevated LCN2 is the cause or consequence of ischemic stroke. Methods: Laboratory and anamnestic data were collected, which could have a role in development of thrombo-embolic events in patients with ischemic stroke. RNA based method was used to evaluate the relative gene expression level of LCN2. We calculated Odds Ratio (OR) and Confidence Interval (CI) for the association between LCN2 and ischemic stroke. Results: 34 samples were available for evaluation. The LCN 2 relative gene expression level was decreased in 12 cases. In this group, 91% of patients have Atrial Fibrillation (AF) at the time of hospitalisation. The mean LCN2 relative gene expression value was 64.25% (ranges: 34%-115%) in patients with AF. It was significantly lower than in patients with normal sinus rhythm (409.2%; ranges: 127%-1127%; p=0.0003). The elevated LCN2 relative gene expression level significantly (p=0.012) increases the risk of stroke (OR: 12.6) independently from other factors. Conclusions: High LCN2 expression level seems to have strong positive predictive value on ischemic stroke, and may be useful in thrombotic risk stratification of plaque vulnerability in these patients.

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