Silicon Affects The Expression Of Conserved And Novel Cucumber miRNAs In Response To Copper Stres
Autori
Bosnić, DraganaTimotijević, Gordana
Nikolić, Dragana
Samardžić, Jelena
Ostala autorstva
Morić, IvanaĐorđević, Valentina
Konferencijski prilog (Objavljena verzija)
Metapodaci
Prikaz svih podataka o dokumentuApstrakt
Environmental pollution with heavy metals such as copper (Cu) severely hinders optimal
plant growth and development. Silicon (Si) is a plant nutrient that can improve plant health
through diverse mechanisms. microRNAs (miRNAs) are recognized as effective regulators
of various processes in plants, including stress responses, however, their involvement in
Si-protective effect remains unrevealed. To clarify the molecular pathways involved in the
protective effect of Si, small RNA-seq analyses (Illumina Sequencing SE50) was performed
on cucumber plants treated with silicon (Si) alone or with a high concentration of Cu (Cu+Si).
The small RNA tags were mapped to the reference sequence by Bowtie tool, following
no-mismatch or one mismatch criterion, to analyze their expression and distribution.
Identification of known miRNAs among the mapped small RNA tags was accomplished by
miRBase22.0 database. miREvo and mirdeep2 were exploited to predict novel miRNAs by
analyzing the secondary... structure, Dicer cleavage site, and minimum free energy of the
small RNA tags unannotated in the previous steps. The prediction of the target gene of
miRNA was performed by psRobot. Differential expression analysis of two treatments was
done using edgeR, with the default threshold qvalue < 0.05 and |log2(fold change)| > 1.
A total of 71 miRNAs were identified in cucumber plants. Twenty miRNAs that were
significantly differentially expressed, including seven novel miRNAs were clustered to find
similar expression patterns. miR398 and miR408, which are known to target Cu-proteins
important for Cu metabolism and transport, were significantly downregulated in Cu+Si
treatment. In contrast, miR156, miR164, mir167, miR394, and miR477 were upregulated
in Cu+Si. Additionally, two novel miRNAs (Novel_15 and Novel_19) were highly expressed
and specific to Cu+Si, while, the Novel_12 miRNA was specific to Si treatment. The putative
target genes of the differentially expressed miRNAs were subjected to Gene Ontology (GO)
enrichment analysis, which revealed localization and transport as the most significant GO
terms in this study.
Ključne reči:
silicon / copper / plants / sequencing / miRNAsIzvor:
5th Belgrade Bioinformatics Conference, 2024, 74-74Izdavač:
- Belgrade : Institute of Molecular Genetics and Genetic Engineering
Finansiranje / projekti:
- Ministarstvo nauke, tehnološkog razvoja i inovacija Republike Srbije, institucionalno finansiranje - 200042 (Univerzitet u Beogradu, Institut za molekularnu genetiku i genetičko inženjerstvo) (RS-MESTD-inst-2020-200042)
Napomena:
- Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024.
Kolekcije
Institucija/grupa
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Bosnić, Dragana AU - Timotijević, Gordana AU - Nikolić, Dragana AU - Samardžić, Jelena PY - 2024 UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2458 AB - Environmental pollution with heavy metals such as copper (Cu) severely hinders optimal plant growth and development. Silicon (Si) is a plant nutrient that can improve plant health through diverse mechanisms. microRNAs (miRNAs) are recognized as effective regulators of various processes in plants, including stress responses, however, their involvement in Si-protective effect remains unrevealed. To clarify the molecular pathways involved in the protective effect of Si, small RNA-seq analyses (Illumina Sequencing SE50) was performed on cucumber plants treated with silicon (Si) alone or with a high concentration of Cu (Cu+Si). The small RNA tags were mapped to the reference sequence by Bowtie tool, following no-mismatch or one mismatch criterion, to analyze their expression and distribution. Identification of known miRNAs among the mapped small RNA tags was accomplished by miRBase22.0 database. miREvo and mirdeep2 were exploited to predict novel miRNAs by analyzing the secondary structure, Dicer cleavage site, and minimum free energy of the small RNA tags unannotated in the previous steps. The prediction of the target gene of miRNA was performed by psRobot. Differential expression analysis of two treatments was done using edgeR, with the default threshold qvalue < 0.05 and |log2(fold change)| > 1. A total of 71 miRNAs were identified in cucumber plants. Twenty miRNAs that were significantly differentially expressed, including seven novel miRNAs were clustered to find similar expression patterns. miR398 and miR408, which are known to target Cu-proteins important for Cu metabolism and transport, were significantly downregulated in Cu+Si treatment. In contrast, miR156, miR164, mir167, miR394, and miR477 were upregulated in Cu+Si. Additionally, two novel miRNAs (Novel_15 and Novel_19) were highly expressed and specific to Cu+Si, while, the Novel_12 miRNA was specific to Si treatment. The putative target genes of the differentially expressed miRNAs were subjected to Gene Ontology (GO) enrichment analysis, which revealed localization and transport as the most significant GO terms in this study. PB - Belgrade : Institute of Molecular Genetics and Genetic Engineering C3 - 5th Belgrade Bioinformatics Conference T1 - Silicon Affects The Expression Of Conserved And Novel Cucumber miRNAs In Response To Copper Stres EP - 74 SP - 74 UR - https://hdl.handle.net/21.15107/rcub_imagine_2458 ER -
@conference{ author = "Bosnić, Dragana and Timotijević, Gordana and Nikolić, Dragana and Samardžić, Jelena", year = "2024", abstract = "Environmental pollution with heavy metals such as copper (Cu) severely hinders optimal plant growth and development. Silicon (Si) is a plant nutrient that can improve plant health through diverse mechanisms. microRNAs (miRNAs) are recognized as effective regulators of various processes in plants, including stress responses, however, their involvement in Si-protective effect remains unrevealed. To clarify the molecular pathways involved in the protective effect of Si, small RNA-seq analyses (Illumina Sequencing SE50) was performed on cucumber plants treated with silicon (Si) alone or with a high concentration of Cu (Cu+Si). The small RNA tags were mapped to the reference sequence by Bowtie tool, following no-mismatch or one mismatch criterion, to analyze their expression and distribution. Identification of known miRNAs among the mapped small RNA tags was accomplished by miRBase22.0 database. miREvo and mirdeep2 were exploited to predict novel miRNAs by analyzing the secondary structure, Dicer cleavage site, and minimum free energy of the small RNA tags unannotated in the previous steps. The prediction of the target gene of miRNA was performed by psRobot. Differential expression analysis of two treatments was done using edgeR, with the default threshold qvalue < 0.05 and |log2(fold change)| > 1. A total of 71 miRNAs were identified in cucumber plants. Twenty miRNAs that were significantly differentially expressed, including seven novel miRNAs were clustered to find similar expression patterns. miR398 and miR408, which are known to target Cu-proteins important for Cu metabolism and transport, were significantly downregulated in Cu+Si treatment. In contrast, miR156, miR164, mir167, miR394, and miR477 were upregulated in Cu+Si. Additionally, two novel miRNAs (Novel_15 and Novel_19) were highly expressed and specific to Cu+Si, while, the Novel_12 miRNA was specific to Si treatment. The putative target genes of the differentially expressed miRNAs were subjected to Gene Ontology (GO) enrichment analysis, which revealed localization and transport as the most significant GO terms in this study.", publisher = "Belgrade : Institute of Molecular Genetics and Genetic Engineering", journal = "5th Belgrade Bioinformatics Conference", title = "Silicon Affects The Expression Of Conserved And Novel Cucumber miRNAs In Response To Copper Stres", pages = "74-74", url = "https://hdl.handle.net/21.15107/rcub_imagine_2458" }
Bosnić, D., Timotijević, G., Nikolić, D.,& Samardžić, J.. (2024). Silicon Affects The Expression Of Conserved And Novel Cucumber miRNAs In Response To Copper Stres. in 5th Belgrade Bioinformatics Conference Belgrade : Institute of Molecular Genetics and Genetic Engineering., 74-74. https://hdl.handle.net/21.15107/rcub_imagine_2458
Bosnić D, Timotijević G, Nikolić D, Samardžić J. Silicon Affects The Expression Of Conserved And Novel Cucumber miRNAs In Response To Copper Stres. in 5th Belgrade Bioinformatics Conference. 2024;:74-74. https://hdl.handle.net/21.15107/rcub_imagine_2458 .
Bosnić, Dragana, Timotijević, Gordana, Nikolić, Dragana, Samardžić, Jelena, "Silicon Affects The Expression Of Conserved And Novel Cucumber miRNAs In Response To Copper Stres" in 5th Belgrade Bioinformatics Conference (2024):74-74, https://hdl.handle.net/21.15107/rcub_imagine_2458 .