scholarly journals In silico analysis of transcription factor binding sites in promoters of germin-like protein genes in rice

2016 ◽  
Vol 68 (4) ◽  
pp. 863-876 ◽  
Author(s):  
Muhammad Ilyas ◽  
Syed Naqvi ◽  
Tariq Mahmood
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
In Silico ◽  
In Silico Analysis ◽  
Chromosome 8 ◽  
Upstream Region ◽  
Asian Rice ◽  
Homeobox Protein ◽  
Annotation Project ◽  
Tata Box Binding Protein

Germins (GERs) and germin-like proteins (GLPs) play important roles in responses to various stresses; however, their function is still not fully understood. Significant insight into their function can be obtained by analyzing their promoters. In the present study, the 5' upstream promoters (1000 bp) of 43 Asian rice (Oryza sativa var. Japonica) GLP genes were retrieved from the Plant Ensemble, based on the Rice Annotation Project database (RAP-DB). Phylogenetic analysis via MEGA6 showed a narrow genetic background (0.2%) with a Tajima neutrality value (?) of 0.69. Overall, 4234 transcription factor (TF) binding sites (TFBSs) were found on chromosomes 1, 2, 3, 4, 5, 8, 9, 11 and 12 via ?MatInspector? from 90 different TF families using a total of 444 families. Common TFs and DiAlign analyses showed that arabidopsis homeobox protein (AHBP), MYB-like proteins (MYBL) and vertebrate TATA-box-binding protein (VTBP) were the most abundant, common and evolutionarily conserved elements in the upstream region from 0 to -800. Finding their mutual interaction via Farmworker analysis uncovered three new cisregulatory modules (VTBP_VTBP, MYBS_MYBS, and AHBP_VTBP), which appear to be decisive for OsGLP regulation. In silico functional analysis via ModelInspector revealed 77 cis-regulatory modules, each comprised of two elements, among which DOFF_OPAQ_03 and GTBX_MYCL_01 were the most frequent and mostly found on chromosome 8 and 12, indicating that the combinatorial interaction of these elements has a fundamental role in various biological processes. The study revealed the importance of these elements in regulating OsGLP expression that will help in predicting the role of these genes in various stresses, and can have application in biotechnology.

Abstract 121: Pro-inflammatory Cytokine Ifng Modulates Hepatic Sortilin Expression and Lipid Metabolism.

2015 ◽  
Vol 35 (suppl_1) ◽  
Author(s):  
John Pirault ◽  
Konstantinos Polyzos ◽  
Daniel F Ketelhuth ◽  
Göran K Hansson
Keyword(s):  
Lipid Metabolism ◽  
Binding Sites ◽  
In Silico ◽  
In Silico Analysis ◽  
Lipid Uptake ◽  
Regulatory T Lymphocytes ◽  
Inflammatory Conditions ◽  
Ldl Particles ◽  
Inflammatory Milieu

Rationale: Hypercholesterolemia and immunity are two major risk factors for cardiovascular diseases (CVDs). Yet, we reported increased atherosclerosis upon depletion of regulatory T lymphocytes (Tregs). The effect was associated with increased hepatic inflammation and reduction of Sortilin expression and lipid uptake in the liver. Objective: To define how inflammatory milieu in the liver can modulate Sortilin and lipid metabolism. Methods: To reproduce the inflammatory milieu, hepatocytes (AML-12) were treated in vitro with IFNg. Expression of genes and proteins of interest were followed by qPCR and western blot. In silico method was used to find binding sites of signal transducer and activator of transcription (STAT1) on Sortilin, confirmed later by chromatin immune precipitation assays (Chip). Lipid uptake by hepatocytes was assessed via incubation of cells with radioactive lipoproteins. Results: Culture of AML-12 cells with IFNg induced the phosphorylation of STAT1 showing an active signaling pathway. In the same inflammatory conditions, Sort1 mRNA is decreased meanwhile its inhibitor (Atf3) expression is increased. Kinetic experiments revealed the reduction of Sortilin after 12 hours of culture, suggesting a post-transcriptional regulation of Sort1 by STAT1. In silico analysis revealed putative binding sites for STAT1 on Sortilin gene which was confirmed by chromatin immunoprecipitation assay (Chip). IFNg treated hepatocytes that were incubated with radioactive lipoproteins demonstrated a reduced uptake capacity of VLDL and LDL particles compared to control cultures. Conclusion: All together, these results suggest that inflammation through production of IFNg is able to directly modulate the lipid metabolism in hepatocytes by acting on Sortilin expression.

scholarly journals Homology Modeling and Characterization of Novel Stress Inducing Genes and their Split Sites Recognition in the Genome of Zebra Fish (Danio Rario) by Employing Special Consensus Pattern Matching Algorithms- using an in-Silico Method.

2019 ◽  
Vol 9 (1) ◽  
pp. 6715-6720
Keyword(s):  
Transcription Factor ◽  
Heat Shock ◽  
Pattern Matching ◽  
Binding Sites ◽  
In Silico ◽  
3D Structure ◽  
Transcription Factor Binding Sites ◽  
Heat Shock Transcription Factor ◽  
Zebra Fish ◽  
Transcription Factor 1

Zebra fish has long been considered to be as a strong animal model in biology and modern genetics; however now a days its gaining lot of importance in environmental studies as well. The readily availability of entire genome sequences made to permit carrying out in silico studies at Genomic level. As everyone is known that stress is much more complex and complicated process that involves so much of gene regulations known as up regulation and down regulation, the corresponding stress proteins, broadly known as heat shock proteins. In the current study, the potential transcription factor binding sites were traced out by using bioinformatics tools and about 50 heat shock protein genes were predicted by using special alogorithms using pattern matching and position weight matrices. The 3D structure of DNA-binding domain of HSTF-1 ( Heat Shock Transcription factor-1) which is crucial for regulating heat shot proteins was traced out and builted by using homology modelling methods. The 3D structure of the heat shock transcription factor-1 and together with predicted transcription factor binding sites may be validated in future experimental works which would help us in understanding the complex responsive stress mechanisms lying in Zebra fish.

scholarly journals Comparative in silico analysis identifies bona fide MyoD binding sites within the Myocyte Stress 1 gene promoter

2008 ◽  
Vol 9 (1) ◽  
pp. 50 ◽  
Author(s):  
Samir Ounzain ◽  
Caroline S Dacwag ◽  
Nilesh J Samani ◽  
Anthony N Imbalzano ◽  
Nelson W Chong
Keyword(s):  
Binding Sites ◽  
In Silico ◽  
Gene Promoter ◽  
In Silico Analysis ◽  
Bona Fide ◽  
Silico Analysis

In silico analysis of hnRNP K binding sites in p21 mRNA

2010 ◽  
Vol 68 ◽  
pp. e354
Author(s):  
Mana Igarashi ◽  
Shingo Nakamura ◽  
Mika Kinoshita ◽  
Hirotaka J. Okano ◽  
Hideyuki Okano
Keyword(s):  
Binding Sites ◽  
In Silico ◽  
In Silico Analysis ◽  
Hnrnp K ◽  
Silico Analysis

scholarly journals IN SILICO ANALYSIS OF THE Dof TRANSCRIPTION FACTOR FAMILY IN Coffea canephora

2018 ◽  
Vol 14 (4) ◽  
pp. 99-111
Author(s):  
Vinícius Garcia ◽  
Alessandra Ferreira Ribas ◽  
Luiz Gonzaga Esteves Vieira ◽  
Tiago Benedito dos Santos
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
In Silico ◽  
In Silico Analysis ◽  
Coffea Canephora ◽  
Transcription Factor Family ◽  
Dof Transcription Factor ◽  
Silico Analysis

A família Dof(DNA-binding with One Finger) é um grupo de fatores de transcrição que desempenham papéis importantes no crescimento, desenvolvimento e na resposta das plantas aos estresses bióticos e abióticos. Os genes Dofforam identificados e caracterizados em várias espécies de plantas;entretanto até o presente momento não há informações sobre esses genes em café. No presente estudo foram identificados 24 membros da família Dofno genoma de C. canephoradepositados no banco de dados Coffee Genome Hub. Análises sistemáticas de bioinformática foram realizadas para caracterizar os genes DofemC. canephora, incluindo a análise desequênciasgenômicas, domínios proteicos conservados, localizações subcelulares, relações filogenéticas e perfis de expressão gênica em diferentes tecidos. Os resultados obtidos fornecem uma melhor compreensãosobre a família dos genes CcDofpermitindo projetar experimentos futuros para caracterização molecular dessesgenes no cafeeiro.

scholarly journals In Silico Analysis of Fungal and Chloride-Dependent α-Amylases within the Family GH13 with Identification of Possible Secondary Surface-Binding Sites

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5704
Author(s):  
Zuzana Janíčková ◽  
Štefan Janeček
Keyword(s):  
Binding Sites ◽  
In Silico ◽  
Homo Sapiens ◽  
In Silico Analysis ◽  
Surface Binding ◽  
Conserved Sequence ◽  
Evolutionary Relatedness ◽  
The Family ◽  
Tim Barrel ◽  
Silico Analysis

This study brings a detailed bioinformatics analysis of fungal and chloride-dependent α-amylases from the family GH13. Overall, 268 α-amylase sequences were retrieved from subfamilies GH13_1 (39 sequences), GH13_5 (35 sequences), GH13_15 (28 sequences), GH13_24 (23 sequences), GH13_32 (140 sequences) and GH13_42 (3 sequences). Eight conserved sequence regions (CSRs) characteristic for the family GH13 were identified in all sequences and respective sequence logos were analysed in an effort to identify unique sequence features of each subfamily. The main emphasis was given on the subfamily GH13_32 since it contains both fungal α-amylases and their bacterial chloride-activated counterparts. In addition to in silico analysis focused on eventual ability to bind the chloride anion, the property typical mainly for animal α-amylases from subfamilies GH13_15 and GH13_24, attention has been paid also to the potential presence of the so-called secondary surface-binding sites (SBSs) identified in complexed crystal structures of some particular α-amylases from the studied subfamilies. As template enzymes with already experimentally determined SBSs, the α-amylases from Aspergillus niger (GH13_1), Bacillus halmapalus, Bacillus paralicheniformis and Halothermothrix orenii (all from GH13_5) and Homo sapiens (saliva; GH13_24) were used. Evolutionary relationships between GH13 fungal and chloride-dependent α-amylases were demonstrated by two evolutionary trees—one based on the alignment of the segment of sequences spanning almost the entire catalytic TIM-barrel domain and the other one based on the alignment of eight extracted CSRs. Although both trees demonstrated similar results in terms of a closer evolutionary relatedness of subfamilies GH13_1 with GH13_42 including in a wider sense also the subfamily GH13_5 as well as for subfamilies GH13_32, GH13_15 and GH13_24, some subtle differences in clustering of particular α-amylases may nevertheless be observed.

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