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Khan AA, Ali MS, Babar F, Fatima A, Shafqat MA, Asghar B, Ilyas N, Fatima M, Liaqat A, Gondal MA. Lack of CpG islands in human unitary pseudogenes and its implication. Mamm Genome 2021; 32:443-447. [PMID: 34272576 DOI: 10.1007/s00335-021-09893-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/07/2021] [Indexed: 11/24/2022]
Abstract
CpG islands (CGIs) are aggregation of CpG dinucleotides in the promoters of mammalian genes. These CGIs are present in almost all the housekeeping genes and some tissue-specific genes in the mammalian genome. Extensive research has been done on the prevalence and role of CGIs in protein-coding genes. However, little is known about CGIs in pseudogenes. In the current research project, we focused on CGIs in three main classes of pseudogenes e.g., duplicated pseudogenes (DPGs), processed pseudogenes (PPGs), and unitary pseudogenes (UPGs). We discovered a predominant absence of CGIs in the promoters of all three pseudogenes. We also compared the CGI profile of these pseudogenes with their parent genes and found that unitary pseudogenes (UPGs) differ from the DPGs and PPGs in the sense that in the latter, lack of CGIs is a consequential event while in UPGs, this lack of CGIs in their promoters is not a result of pseudogenization process. We also discussed the implication of the results obtained from this comparison. To our knowledge, this is the first-ever study highlighting this aspect of UPGs throwing new insights into the evolution of genome in general and especially in the context of pseudogenes.
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Affiliation(s)
- Ammad Aslam Khan
- Department of Bioinformatics and Computational Biology, Virtual University, Lahore, 547 92, Pakistan.
| | - Muhammad Shahryar Ali
- Department of Bioinformatics and Computational Biology, Virtual University, Lahore, 547 92, Pakistan
| | - Farah Babar
- Department of Bioinformatics and Computational Biology, Virtual University, Lahore, 547 92, Pakistan
| | - Anees Fatima
- Department of Bioinformatics and Computational Biology, Virtual University, Lahore, 547 92, Pakistan
| | - Muhammad Awais Shafqat
- Department of Bioinformatics and Computational Biology, Virtual University, Lahore, 547 92, Pakistan
| | - Bisma Asghar
- Department of Bioinformatics and Computational Biology, Virtual University, Lahore, 547 92, Pakistan
| | - Nimra Ilyas
- Department of Bioinformatics and Computational Biology, Virtual University, Lahore, 547 92, Pakistan
| | - Maheen Fatima
- Department of Bioinformatics and Computational Biology, Virtual University, Lahore, 547 92, Pakistan
| | - Ayesha Liaqat
- Department of Bioinformatics and Computational Biology, Virtual University, Lahore, 547 92, Pakistan
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Babar F, Sarwar S, Ismail MK. GROUP G STREPTOCOCCUS: AN UNUSUAL CAUSE OF ENDOCARDITIS IN AN HIV PATIENT. J Investig Med 2007. [DOI: 10.1097/00042871-200701010-00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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