Open Access Highly Accessed Research article

miR-296-3p, miR-298-5p and their downstream networks are causally involved in the higher resistance of mammalian pancreatic α cells to cytokine-induced apoptosis as compared to β cells

Davide Barbagallo1, Salvatore Piro2, Angelo G Condorelli1, Loriana G Mascali2, Francesca Urbano2, Nunziatina Parrinello2, Adelina Monello2, Luisa Statello1, Marco Ragusa1, Agata M Rabuazzo2, Cinzia Di Pietro1, Francesco Purrello2* and Michele Purrello1*

Author Affiliations

1 Dipartimento Gian Filippo Ingrassia, Unità di BioMedicina Molecolare Genomica e dei Sistemi Complessi, Genetica, Biologia Computazionale, Università di Catania, Catania, EU 95123, Italy

2 Dipartimento di BioMedicina Clinica e Molecolare, Università di Catania, Catania, EU 95122, Italy

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BMC Genomics 2013, 14:62  doi:10.1186/1471-2164-14-62

Published: 29 January 2013

Additional files

Additional file 1:

DE miRNAs between αTC1-6 and βTC1 at steady state.

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Additional file 2:

Classification in families of miRNAs more abundantly or exclusively expressed in αTC1-6 respect to βTC1 at steady state.

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Additional file 3:

Classification in families of miRNAs more abundantly or exclusively expressed in βTC1 with respect to αTC1-6 at steady state.

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Additional file 4:

αTC1-6 DE miRNAs after 24 and 48 h of treatment with cytokines. In bold are indicated significant DE miRNAs (adjusted p-values < 0.05. Limma Test, Benjamini-Hochberg correction). MiRNAs are ranked based on increasing adjusted p-values (from the most to the least significant DE miRNAs).

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Additional file 5:

Classification in families of DE miRNAs in αTC1-6 after treatment with cytokines.

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Additional file 6:

Scatter plot showing correlation between miR-296-3p (x-axis) and miR-298-5p (y-axis) expression in αTC1-6, during a 6-12-24-48 h time-course experiment. For each time point DCt values of miR-296-3p and miR-298-5p were correlated, both from untreated and cytokines-treated αTC1-6 cells (r-value = 0.88, p-value = 1.15e-08, Pearson’s correlation test). Three independent biological replicates (n = 3) have been analyzed at each time point.

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Additional file 7:

On scale representation of the genome segment comprisingNespas, miR-296, miR-298. CpG islands are indicated as red vertical lines; pre-miRNAs 296 and 298 are depicted as blue and green boxes, respectively; exons of noncoding RNA Nespas are shown as yellow boxes. Expression of a macro-noncoding RNA (precursor of miR-296, miR-298, Nespas) is predicted to be controlled by two groups of CpG islands (one comprising two CpG islands, from 17.5 to 18.8 kb upstream the first nucleotide of pre-miR-296; the other made of three CpG islands, from 30.1 to 33.6 Kb upstream the first nucleotide of pre-miR-296).

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Additional file 8:

Validated and predicted targets of miR-296-3p and miR-298-5p. A selection of validated and predicted targets of miR-296-3p and miR-298-5p was chosen according to their involvement in apoptosis, cell cycle progression, cell differentiation and hormone secretion.

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Additional file 9:

Interaction network among miRNAs more abundantly expressed at steady state in αTC1-6 with respect to βTC1, their validated targets and first neighbours interactants. The network generated from validated targets and first neighbours interactants of 14 out of 50 miRNAs, more abundantly expressed at steady state in αTC1-6 with respect to βTC1, consisted of 560 nodes and 8222 edges. MiRNAs are represented as fuchsia diamonds. This file can be opened and browsed through Cytoscape tool and its plugins (http://www.cytoscape.org/ webcite).

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Additional file 10:

Interaction network among miRNAs specifically expressed at steady state in αTC1-6 (α-miRNAs) with respect to βTC1, their validated targets and first neighbours interactants. The network generated from validated targets and first neighbours interactants of 4 out of 23 α-miRNAs consisted of 117 nodes and 530 edges. MiRNAs are represented as fuchsia diamonds. This file can be opened and browsed through Cytoscape tool and its plugins (http://www.cytoscape.org/ webcite).

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Additional file 11:

Interaction network among miRNAs more abundantly expressed at steady state in βTC1 with respect to αTC1-6, their validated targets and first neighbours interactants. The network generated from validated targets and first neighbours interactants of 36 of 74 miRNAs more abundantly expressed at steady state in βTC1 with respect to αTC1-6 consisted of 439 nodes and 2079 edges. MiRNAs are represented as fuchsia diamonds. This file can be opened and browsed through Cytoscape tool and its plugins (http://www.cytoscape.org/ webcite).

Format: CYS Size: 56KB Download file

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Additional file 12:

Interaction network among miRNAs specifically expressed at steady state in βTC1-6 (β-miRNAs) with respect to αTC1-6, their validated targets and first neighbours interactants. The network generated from validated targets and first neighbours interactants of 15 of 26 β-miRNAs consisted of 107 nodes and 132 edges. MiRNAs are represented as fuchsia diamonds. This file can be opened and browsed through Cytoscape tool and its plugins (http://www.cytoscape.org/ webcite).

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Additional file 13:

Hypothetical model of regulation of miR-296-3p and miR-298-5p biomolecular activity in αTC1-6 at steady state (left) and after treatment with cytokines (right).

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Additional file 14:

Additional Methods.

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