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Huntington's chorea, a neurological disorder of all ages - Bioinformatics approach for its precise diagnosis
Krupanidhi Srirama1, J Vineela1, K Tejaswi1
1Department of Biotechnology, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Andhra Pradesh, India.
Insights
Bioinformatics tools identified defects in the Huntington
Area of Science:
- Genetics
- Bioinformatics
- Molecular Biology
Background:
- Huntington's disease (HD) is a neurodegenerative disorder impacting social mobility.
- Understanding HD's molecular basis and utilizing bioinformatics are crucial for diagnosis and patient care.
- Community-level support for HD patients is increasing due to reduced social stigma.
Purpose of the Study:
- To investigate bioinformatics tools for identifying defects in the Huntington's gene (HTT).
- To design a small-guided RNA (sgRNA) for potential therapeutic applications in HD.
Main Methods:
- Retrieved HTT gene sequence and identified CRISPR sites using the UCSC Genome Browser.
- Determined sgRNA sequence and elucidated HTT protein structure via PDB and Swiss-Model.
- Analyzed HTT protein's poly-Q region using Ramachandran plots via the Rampage tool.
Main Results:
- CRISPR sites and sgRNA sequences for the HTT gene were successfully identified using the UCSC Genome Browser.
- The HTT protein structure is predominantly alpha-helical, with polyglutamine (poly-Q) clusters identified in specific regions.
- The obtained sgRNA sequence is intended for future genome editing applications with Cas9.
Conclusions:
- Bioinformatics tools like UCSC Genome Browser, Swiss-Model, and Rampage are valuable for studying HD's molecular underpinnings.
- These tools aid in understanding the disease-causing HTT protein structure and poly-Q repeat expansions.
- Such analyses can contribute to increased awareness and improved care strategies for Huntington's disease patients.
Background:
The disease that obstructs social movements of people is Huntington's disease (HD). Hence, the expedition of its molecular aspects and bioinformatics tools relating to precise confirmation of the disease is warranted. Due to social stigma, the care and attention to safeguard these patients had increased at community level.
Objective:
The objective of the study was to explore bioinformatics tools to trace the defects in Huntington's gene and design its small-guided RNA (sgRNA).
Methodology:
The HTT gene sequence was retrieved, CRISPR sites were identified, and gRNA sequence was determined using the University of California Santa Cruz (UCSC) Genome Browser. HTT protein molecular structure elucidation was retrieved through PDB and Swiss Model. Ramachandran plot displayed the cluster of poly-Q at the Phi (-60--36) and Psi (-60--65) regions. The pattern of residues in the plot displayed that the HTT protein is alpha-helical predominant.
Results:
The CRISPR sites on HTT gene are viewed and sgRNA sequences are obtained through the UCSC Genome Browser. This sgRNA sequence along with Cas9 would be planned for genome editing in future experimental models. The Ramachandran plot for HTT protein derived through online Rampage revealed the recurrent appearance of polyglutamine (Q) at the Phi (-55--65) and Psi (120-135) regions.
Conclusion:
Online bioinformatic tools such as UCSC Genome Browser, Swiss-Model, and Rampage help in exploring molecular basis of HD and disease-causing protein HTT, and the same invariably assists in creating awareness among health workers.
