BioGPS has become the valuable resource that it is because of the contributions from our wonderful user community. Thank you for contributing plugins, suggestions, and ideas–all of which have improved BioGPS for everyone. In order to celebrate the contributions of BioGPS users to the scientific research community, this series will feature publications and articles generated by BioGPS users. We sincerely hope you will join us in celebrating the fascinating work that YOU do.
This week, we will feature an article from a group that performs intriguing research investigating the relationship between the circadium rhythm and cardiovascular physiology: Circadian Regulation of Myocardial Sarcomeric Titin-cap (Tcap, Telethonin): Identification of Cardiac Clock-Controlled Genes Using Open Access Bioinformatics Data by Peter S. Podobed, Faisal J. Alibhai, Chi-Wing Chow, Tami A. Martino. (DOI 10.1371/journal.pone.0104907)
Dr. Tami A. Martino kindly answered our inquiries for this series.
- Who is the team behind the work that was published in Circadian Regulation of Myocardial Sarcomeric Titin-cap (Tcap, Telethonin): Identification of Cardiac Clock-Controlled Genes Using Open Access Bioinformatics Data?
This work was conducted by Dr. Tami Martino’s laboratory from the Cardiovascular Research Group, Department of Biomedical Sciences, University of Guelph, Canada in collaboration with Dr. Chi-Wing Chow at the Department of Pharmacology, Albert Einstein College of Medicine, U.S.
- Please provide a brief summary of your research findings from Circadian Regulation of Myocardial Sarcomeric Titin-cap (Tcap, Telethonin): Identification of Cardiac Clock-Controlled Genes Using Open Access Bioinformatics Data.
Circadian rhythms are crucial for healthy cardiovascular physiology and are regulated at the molecular level by a circadian clock mechanism. However, the genes directly regulated by the circadian clock mechanism in the heart are not known. In this study, we first used open access bioinformatics databases to identify cardiac genes controlled by the core clock transcription factors CLOCK and BMAL1. We used CircaDB website and JTK_Cycle algorithm to identify 94 transcripts with expression profiles characteristic of CLOCK and BMAL1 targeted genes. Then, we used BioGPS to select 22 highly expressed genes in the heart. Then we identified which of these genes had phylogenetically conserved E-box elements between mouse and human using UCSC table browser, circadian mammalian promoter/enhancer database (PEDB), and the European Bioinformatics Institute alignment tool (EMBOSS). Next, we experimentally validated our bioinformatics approach by demonstrating that Titin cap (Tcap, telethonin) was targeted by transcriptional activators CLOCK and BMAL1. Clock regulation of Tcap is especially interesting because Tcap is a key protein in the for sarcomere structure and function – the main contractility apparatus that allow heart cells to beat. This study was the first to demonstrate direct regulation of a sarcomere protein by the circadian clock mechanism.
- How did the team learn about and/or utilize BioGPS for this research?
We used BioGPS Gene expression/activity chart to identify genes with high level of cardiac expression (heart enriched genes). We also used Gene Identifiers module to retrieve Gene Ontology (GO) classifications.
- What are some future directions for the team behind this research?
The overall goal of our research is to understand circadian regulation of the cardiovascular system, leading to new translational approaches to benefit patients with heart disease.
Thanks again to Dr. Tami A. Martino for answering our questions. Click here to read their fascinating article. Have a look because these awesome researchers not only utilized open access bioinformatics for their work, they also contributed back to open science by making this article open access–so you can read the whole exciting article for free!
Used BioGPS and cited it in your publication? Let us know! We would love to feature YOUR work, no matter how long ago it was published. BioGPS Featured Article Series only started recently, but we know your contributions to science is ongoing.
2016.06.16 – Links in this post were updated to lead to the original article