Identification and Characterization of Cis-Regulatory Elements ‘Insulator and Repressor’ in PPARD Gene

Abstract

Aim: Identification and functional characterization of cis-regulatory elements in human PPARD gene. Methods: We used various bioinformatic tools on the publicly available human genome and Encyclopedia of DNA Elements databases to explore potential cis-regulatory elements in PPARD gene region. Results: We predicted an insulator and an enhancer element in intron 2 of PPARD gene. Functional characterization using transient transfection, reporter assay and CTCF binding confirmed the insulator status. However, the predicted enhancer element showed repressor/silencer activity. Finally, we observed a potential interaction between these two cis-regulatory elements which is in agreement with 5C-Encyclopedia of DNA Elements data. Conclusion: We report two functionally validated cis-regulatory elements in PPARD gene which will aid in understanding its regulation and role in metabolic functions.

Keywords::

• cis-regulatory elements
• ENCODE
• enhancer
• insulator
• peroxisome proliferator-activated receptor beta/delta
• repressor
• Type 2 diabetes

Supplementary data

To view the supplementary data that accompany this paper, please visit the journal website at:

https://www.tandfonline.com/doi/suppl/10.2217/epi-2017-0139

Author’s contributions

GR Chandak conceptualized and planned the study with significant intellectual contribution from DK Yadav and S Shrestha. S Shrestha contributed to the bioinformatic analysis. DK Yadav also performed all functional experiments with assistance from G Dadhwal and wrote the first draft of the manuscript. All authors read and provided critical comments on the manuscript. GR Chandak is the guarantor of this work and, as such, had full access to all the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.

Acknowledgements

The authors acknowledge the infrastructure support of CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.

Financial & competing interests disclosure

This work was supported by funds from Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, India (BT/IN/Denmark/02/CSY/2014). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. DK Yadav also acknowledges the financial support of Council of Scientific and Industrial Research (CSIR), Ministry of Science and Technology, Government of India, India (XIIFive-Year Plan titled “EpiHED; BSC0118”). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

This work was supported by funds from Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, India (BT/IN/Denmark/02/CSY/2014). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. DK Yadav also acknowledges the financial support of Council of Scientific and Industrial Research (CSIR), Ministry of Science and Technology, Government of India, India (XIIFive-Year Plan titled “EpiHED; BSC0118”). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.