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Biochemical Genetics

, Volume 54, Issue 3, pp 211–221 | Cite as

A Bioinformatics Approach to the Identification of Variants Associated with Type 1 and Type 2 Diabetes Mellitus that Reside in Functionally Validated miRNAs Binding Sites

  • Hamid Ghaedi
  • Milad Bastami
  • Mohammad Mehdi Jahani
  • Behnam Alipoor
  • Maryam Tabasinezhad
  • Omar Ghaderi
  • Ziba Nariman-Saleh-Fam
  • Reza Mirfakhraie
  • Abolfazl Movafagh
  • Mir Davood Omrani
  • Andrea Masotti
Original Article

Abstract

The present work is aimed at finding variants associated with Type 1 and Type 2 diabetes mellitus (DM) that reside in functionally validated miRNAs binding sites and that can have a functional role in determining diabetes and related pathologies. Using bioinformatics analyses we obtained a database of validated polymorphic miRNA binding sites which has been intersected with genes related to DM or to variants associated and/or in linkage disequilibrium (LD) with it and is reported in genome-wide association studies (GWAS). The workflow we followed allowed us to find variants associated with DM that also reside in functional miRNA binding sites. These data have been demonstrated to have a functional role by impairing the functions of genes implicated in biological processes linked to DM. In conclusion, our work emphasized the importance of SNPs located in miRNA binding sites. The results discussed in this work may constitute the basis of further works aimed at finding functional candidates and variants affecting protein structure and function, transcription factor binding sites, and non-coding epigenetic variants, contributing to widen the knowledge about the pathogenesis of this important disease.

Keywords

Diabetes mellitus Genome-wide association study MicroRNA Single nucleotide polymorphism Target site 

Notes

Acknowledgments

We thank Shahid Beheshti University of Medical Sciences for providing the fund of this work (Fund Number: 1393-1-91-13285). Also this work was supported partly by Italian Ministry of Health by providing financial support to Andrea Masotti (Ricerca Corrente 2014 and 2015).

Supplementary material

10528_2016_9713_MOESM1_ESM.docx (56 kb)
Supplementary material 1 (DOCX 56 kb)
10528_2016_9713_MOESM2_ESM.docx (27 kb)
Supplementary material 2 (DOCX 26 kb)

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Hamid Ghaedi
    • 1
  • Milad Bastami
    • 1
  • Mohammad Mehdi Jahani
    • 2
  • Behnam Alipoor
    • 3
  • Maryam Tabasinezhad
    • 4
  • Omar Ghaderi
    • 5
  • Ziba Nariman-Saleh-Fam
    • 6
  • Reza Mirfakhraie
    • 1
  • Abolfazl Movafagh
    • 1
  • Mir Davood Omrani
    • 1
  • Andrea Masotti
    • 7
  1. 1.Medical Genetics Department, Faculty of MedicineShahid Beheshti University of Medical SciencesTehranIran
  2. 2.Faculty of VeterinaryShahrekord Islamic Azad UniversityShahrekordIran
  3. 3.Clinical Biochemistry Department, Faculty of MedicineTehran University of Medical SciencesTehranIran
  4. 4.Medical Biotechnology DepartmentPasteur Institute of IranTehranIran
  5. 5.Department of Pharmaceutical Biotechnology, Faculty of PharmacyTehran University of Medical SciencesTehranIran
  6. 6.Medical Genetics Department, Faculty of MedicineTehran University of Medical SciencesTehranIran
  7. 7.Gene Expression - Microarrays LaboratoryBambino Gesù Children’s Hospital, IRCCSRomeItaly

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