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Hypothetical Proteins as Predecessors of Long Non-coding RNAs.
Girik Malik1, Tanu Agarwal1, Utkarsh Raj1
11Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India.
Hypothetical Proteins (HP) may represent evolutionary precursors to long non-coding RNAs (lncRNAs). This commentary explores the potential role of HP open reading frames in understanding genome annotation and the origins of lncRNAs.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Hypothetical Proteins (HP) are predicted transcripts lacking experimental evidence.
- Long non-coding RNAs (lncRNAs) are transcripts >200 bases in UTR or intergenic regions.
- Genomes contain 'known unknown' [KU] regions requiring functional annotation.
Purpose of the Study:
- To propose that Hypothetical Proteins could be precursors to lncRNAs.
- To highlight the importance of open reading frames in genome annotation.
- To bridge the understanding between uncharacterized transcripts and functional RNAs.
Main Methods:
- Conceptual analysis and literature review.
- Comparative genomics perspective.
- Bioinformatic annotation strategies.
Main Results:
- HP represent a potential source of novel lncRNA discovery.
- Open reading frames in KU regions warrant further investigation.
- A theoretical framework linking HP to lncRNA evolution is presented.
Conclusions:
- HP may serve as evolutionary predecessors of lncRNAs.
- Understanding HP function is crucial for comprehensive genome annotation.
- This perspective aids in deciphering the functional landscape of non-coding genomic regions.
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