Complexity driven evolution of Alternative splicing
Конференцијски прилог (Објављена верзија)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
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Based on the animal model of agonistic interactions, we observed co-varied (linked)
alternative exons (LEs) in the genes with alternative splicing phenotype in brain. As a result,
we have found 263 positively co-varied pairs, and 26 pairs with negative co-variation. To
ascertain the data consistency, we employed three organisms cross-validation: human,
mouse and rat with available hippocampus brain region SRA repositories, which supported
the co-varied effect of the corresponding exons.
From 142 genes with LE events the maximum LE pairs were observed in insulin – related
Sorbs1 (Sorbin And SH3 Domain Containing 1; 18 LE AS events), and synaptic Nrcam (12
LE events). 104 genes maintain only 1 LE pair and 36 genes maintain 2-7 LE pairs. Notably
there is a mode at 3 LE pairs per gene (14 genes) in genes vs LE events distribution. GO
analysis reveals that the majority of genes maintaining LE events have belong to the
synaptic genes, RNA-splicing machinery, and chromatin remodeli...ng.
The ‘complexity’ (entropic) measure of gene is calculated as Σ
=
−
i 1,n
ψ log 2(ψ ) ,
where (Ψ) psi is a percent inclusion rate of a particular AS exon, n – number of AS
exons in the gene. It is evident that linked AS exons decrease gene complexity rate [3],
allowing coordinated splicing in high splicing dynamics rate genes, such as synaptic,
RNA processing, chromatin remodeling genes. Herein we speculate if LE AS events are
of evolutionary advantage for the high splicing turnover genes working in homeostasis
equilibrium.
Next step of the work is to elucidate features providing the linking phenomenon, including
mRNA secondary structure, the splicing factor binding sites within and around the
corresponding exons.
We will present the results on the issue featuring some complex interactions between
exons.
Кључне речи:
alternative splicing / entropy / evolutionИзвор:
4th Belgrade Bioinformatics Conference, 2023, 4, 19-19Издавач:
- Belgrade : Institute of molecular genetics and genetic engineering
Финансирање / пројекти:
- The study was supported by the Russian Science Foundation (grant no. 19-15-00026).
Напомена:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Колекције
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Babenko, Vladimir AU - Boltunov, Timophey PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1954 AB - Based on the animal model of agonistic interactions, we observed co-varied (linked) alternative exons (LEs) in the genes with alternative splicing phenotype in brain. As a result, we have found 263 positively co-varied pairs, and 26 pairs with negative co-variation. To ascertain the data consistency, we employed three organisms cross-validation: human, mouse and rat with available hippocampus brain region SRA repositories, which supported the co-varied effect of the corresponding exons. From 142 genes with LE events the maximum LE pairs were observed in insulin – related Sorbs1 (Sorbin And SH3 Domain Containing 1; 18 LE AS events), and synaptic Nrcam (12 LE events). 104 genes maintain only 1 LE pair and 36 genes maintain 2-7 LE pairs. Notably there is a mode at 3 LE pairs per gene (14 genes) in genes vs LE events distribution. GO analysis reveals that the majority of genes maintaining LE events have belong to the synaptic genes, RNA-splicing machinery, and chromatin remodeling. The ‘complexity’ (entropic) measure of gene is calculated as Σ = − i 1,n ψ log 2(ψ ) , where (Ψ) psi is a percent inclusion rate of a particular AS exon, n – number of AS exons in the gene. It is evident that linked AS exons decrease gene complexity rate [3], allowing coordinated splicing in high splicing dynamics rate genes, such as synaptic, RNA processing, chromatin remodeling genes. Herein we speculate if LE AS events are of evolutionary advantage for the high splicing turnover genes working in homeostasis equilibrium. Next step of the work is to elucidate features providing the linking phenomenon, including mRNA secondary structure, the splicing factor binding sites within and around the corresponding exons. We will present the results on the issue featuring some complex interactions between exons. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Complexity driven evolution of Alternative splicing EP - 19 SP - 19 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_1954 ER -
@conference{ author = "Babenko, Vladimir and Boltunov, Timophey", year = "2023", abstract = "Based on the animal model of agonistic interactions, we observed co-varied (linked) alternative exons (LEs) in the genes with alternative splicing phenotype in brain. As a result, we have found 263 positively co-varied pairs, and 26 pairs with negative co-variation. To ascertain the data consistency, we employed three organisms cross-validation: human, mouse and rat with available hippocampus brain region SRA repositories, which supported the co-varied effect of the corresponding exons. From 142 genes with LE events the maximum LE pairs were observed in insulin – related Sorbs1 (Sorbin And SH3 Domain Containing 1; 18 LE AS events), and synaptic Nrcam (12 LE events). 104 genes maintain only 1 LE pair and 36 genes maintain 2-7 LE pairs. Notably there is a mode at 3 LE pairs per gene (14 genes) in genes vs LE events distribution. GO analysis reveals that the majority of genes maintaining LE events have belong to the synaptic genes, RNA-splicing machinery, and chromatin remodeling. The ‘complexity’ (entropic) measure of gene is calculated as Σ = − i 1,n ψ log 2(ψ ) , where (Ψ) psi is a percent inclusion rate of a particular AS exon, n – number of AS exons in the gene. It is evident that linked AS exons decrease gene complexity rate [3], allowing coordinated splicing in high splicing dynamics rate genes, such as synaptic, RNA processing, chromatin remodeling genes. Herein we speculate if LE AS events are of evolutionary advantage for the high splicing turnover genes working in homeostasis equilibrium. Next step of the work is to elucidate features providing the linking phenomenon, including mRNA secondary structure, the splicing factor binding sites within and around the corresponding exons. We will present the results on the issue featuring some complex interactions between exons.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Complexity driven evolution of Alternative splicing", pages = "19-19", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_1954" }
Babenko, V.,& Boltunov, T.. (2023). Complexity driven evolution of Alternative splicing. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 19-19. https://hdl.handle.net/21.15107/rcub_imagine_1954
Babenko V, Boltunov T. Complexity driven evolution of Alternative splicing. in 4th Belgrade Bioinformatics Conference. 2023;4:19-19. https://hdl.handle.net/21.15107/rcub_imagine_1954 .
Babenko, Vladimir, Boltunov, Timophey, "Complexity driven evolution of Alternative splicing" in 4th Belgrade Bioinformatics Conference, 4 (2023):19-19, https://hdl.handle.net/21.15107/rcub_imagine_1954 .