Genome biology of long non-coding RNAs in humans: A virtual karyotype
Long non-coding RNAs (lncRNAs) represent a groundbreaking class of RNA molecules that exert regulatory functions with remarkable tissue and cellular specificity. Although the identification of functionally significant lncRNAs is increasing, a comprehensive profiling of their genomic features remains...
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| Language: | English |
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Elsevier
2025-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S200103702500025X |
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| author | Alessandro Palma Giulia Buonaiuto Monica Ballarino Pietro Laneve |
| author_facet | Alessandro Palma Giulia Buonaiuto Monica Ballarino Pietro Laneve |
| author_sort | Alessandro Palma |
| collection | DOAJ |
| description | Long non-coding RNAs (lncRNAs) represent a groundbreaking class of RNA molecules that exert regulatory functions with remarkable tissue and cellular specificity. Although the identification of functionally significant lncRNAs is increasing, a comprehensive profiling of their genomic features remains elusive. Here, we present a detailed overview of the distribution of lncRNA genes across human chromosomes and describe key RNA features—what we refer to as a “virtual lncRNA karyotype”—that provide insights into their biosynthesis and function. To achieve this, we leveraged existing human annotation files to construct a statistical genomic portrait of lncRNAs in comparison with protein-coding genes (PCGs). We found that lncRNAs are unevenly distributed across chromosomes and identified regions of high lncRNA density on chromosomes 18, 13, and X, which overlap with PCG-rich regions. Additionally, we observed that lncRNAs generally exhibit shorter gene lengths and fewer splicing variants compared to protein-coding transcripts, with a subset displaying pronounced clustering patterns that may indicate functional relevance. Finally, we identified several clinically associated and experimentally validated SNPs impacting lncRNA genes (lncGs). Overall, this study provides a foundational reference for exploring the non-coding genome, offering new insights into the genomic characteristics of lncRNAs. These findings may enhance our understanding of their biological significance and potential roles in disease. |
| format | Article |
| id | doaj-art-369a34fcebd243e485578fc7e7e8036e |
| institution | Kabale University |
| issn | 2001-0370 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj-art-369a34fcebd243e485578fc7e7e8036e2025-02-06T05:11:31ZengElsevierComputational and Structural Biotechnology Journal2001-03702025-01-0127575584Genome biology of long non-coding RNAs in humans: A virtual karyotypeAlessandro Palma0Giulia Buonaiuto1Monica Ballarino2Pietro Laneve3Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy; Corresponding author.Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, ItalyDepartment of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, ItalyDepartment of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy; Institute of Molecular Biology and Pathology, National Research Council of Italy, Piazzale Aldo Moro 7, Rome 00185, Italy; Corresponding author at: Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.Long non-coding RNAs (lncRNAs) represent a groundbreaking class of RNA molecules that exert regulatory functions with remarkable tissue and cellular specificity. Although the identification of functionally significant lncRNAs is increasing, a comprehensive profiling of their genomic features remains elusive. Here, we present a detailed overview of the distribution of lncRNA genes across human chromosomes and describe key RNA features—what we refer to as a “virtual lncRNA karyotype”—that provide insights into their biosynthesis and function. To achieve this, we leveraged existing human annotation files to construct a statistical genomic portrait of lncRNAs in comparison with protein-coding genes (PCGs). We found that lncRNAs are unevenly distributed across chromosomes and identified regions of high lncRNA density on chromosomes 18, 13, and X, which overlap with PCG-rich regions. Additionally, we observed that lncRNAs generally exhibit shorter gene lengths and fewer splicing variants compared to protein-coding transcripts, with a subset displaying pronounced clustering patterns that may indicate functional relevance. Finally, we identified several clinically associated and experimentally validated SNPs impacting lncRNA genes (lncGs). Overall, this study provides a foundational reference for exploring the non-coding genome, offering new insights into the genomic characteristics of lncRNAs. These findings may enhance our understanding of their biological significance and potential roles in disease.http://www.sciencedirect.com/science/article/pii/S200103702500025XLong non-coding RNAGenomicsChromosomesSNPsFunctional genomics |
| spellingShingle | Alessandro Palma Giulia Buonaiuto Monica Ballarino Pietro Laneve Genome biology of long non-coding RNAs in humans: A virtual karyotype Computational and Structural Biotechnology Journal Long non-coding RNA Genomics Chromosomes SNPs Functional genomics |
| title | Genome biology of long non-coding RNAs in humans: A virtual karyotype |
| title_full | Genome biology of long non-coding RNAs in humans: A virtual karyotype |
| title_fullStr | Genome biology of long non-coding RNAs in humans: A virtual karyotype |
| title_full_unstemmed | Genome biology of long non-coding RNAs in humans: A virtual karyotype |
| title_short | Genome biology of long non-coding RNAs in humans: A virtual karyotype |
| title_sort | genome biology of long non coding rnas in humans a virtual karyotype |
| topic | Long non-coding RNA Genomics Chromosomes SNPs Functional genomics |
| url | http://www.sciencedirect.com/science/article/pii/S200103702500025X |
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