Functional inference of long non-coding RNAs through exploration of highly conserved regions
Background: Long non-coding RNAs (lncRNAs), which are generally less functionally characterized or less annotated, evolve more rapidly than mRNAs and substantially possess fewer sequence conservation patterns than protein-coding genes across divergent species. People assume that the functional infer...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1177259/full |
| _version_ | 1797826289479974912 |
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| author | Zhongpeng Liu Tianbin Guo Zhuoda Yin Yanluo Zeng Haiwen Liu Hongyan Yin |
| author_facet | Zhongpeng Liu Tianbin Guo Zhuoda Yin Yanluo Zeng Haiwen Liu Hongyan Yin |
| author_sort | Zhongpeng Liu |
| collection | DOAJ |
| description | Background: Long non-coding RNAs (lncRNAs), which are generally less functionally characterized or less annotated, evolve more rapidly than mRNAs and substantially possess fewer sequence conservation patterns than protein-coding genes across divergent species. People assume that the functional inference could be conducted on the evolutionarily conserved long non-coding RNAs as they are most likely to be functional. In the past decades, substantial progress has been made in discussions on the evolutionary conservation of non-coding genomic regions from multiple perspectives. However, understanding their conservation and the functions associated with sequence conservation in relation to further corresponding phenotypic variability or disorders still remains incomplete.Results: Accordingly, we determined a highly conserved region (HCR) to verify the sequence conservation among long non-coding RNAs and systematically profiled homologous long non-coding RNA clusters in humans and mice based on the detection of highly conserved regions. Moreover, according to homolog clustering, we explored the potential function inference via highly conserved regions on representative long non-coding RNAs. On lncRNA XACT, we investigated the potential functional competence between XACT and lncRNA XIST by recruiting miRNA-29a, regulating the downstream target genes. In addition, on lncRNA LINC00461, we examined the interaction relationship between LINC00461 and SND1. This interaction or association may be perturbed during the progression of glioma. In addition, we have constructed a website with user-friendly web interfaces for searching, analyzing, and downloading to present the homologous clusters of humans and mice.Conclusion: Collectively, homolog clustering via the highly conserved region definition and detection on long non-coding RNAs, as well as the functional explorations on representative sequences in our research, would provide new evidence for the potential function of long non-coding RNAs. Our results on the remarkable roles of long non-coding RNAs would presumably provide a new theoretical basis and candidate diagnostic indicators for tumors. |
| first_indexed | 2024-03-13T11:06:34Z |
| format | Article |
| id | doaj.art-83d44102e8b54af18e6e60175ee4f707 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-13T11:06:34Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-83d44102e8b54af18e6e60175ee4f7072023-05-16T05:34:53ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-05-011410.3389/fgene.2023.11772591177259Functional inference of long non-coding RNAs through exploration of highly conserved regionsZhongpeng Liu0Tianbin Guo1Zhuoda Yin2Yanluo Zeng3Haiwen Liu4Hongyan Yin5Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, ChinaHainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, ChinaTJ-YZ School of Network Science, Haikou University of Economics, Haikou, ChinaHainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, ChinaHainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, ChinaHainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, ChinaBackground: Long non-coding RNAs (lncRNAs), which are generally less functionally characterized or less annotated, evolve more rapidly than mRNAs and substantially possess fewer sequence conservation patterns than protein-coding genes across divergent species. People assume that the functional inference could be conducted on the evolutionarily conserved long non-coding RNAs as they are most likely to be functional. In the past decades, substantial progress has been made in discussions on the evolutionary conservation of non-coding genomic regions from multiple perspectives. However, understanding their conservation and the functions associated with sequence conservation in relation to further corresponding phenotypic variability or disorders still remains incomplete.Results: Accordingly, we determined a highly conserved region (HCR) to verify the sequence conservation among long non-coding RNAs and systematically profiled homologous long non-coding RNA clusters in humans and mice based on the detection of highly conserved regions. Moreover, according to homolog clustering, we explored the potential function inference via highly conserved regions on representative long non-coding RNAs. On lncRNA XACT, we investigated the potential functional competence between XACT and lncRNA XIST by recruiting miRNA-29a, regulating the downstream target genes. In addition, on lncRNA LINC00461, we examined the interaction relationship between LINC00461 and SND1. This interaction or association may be perturbed during the progression of glioma. In addition, we have constructed a website with user-friendly web interfaces for searching, analyzing, and downloading to present the homologous clusters of humans and mice.Conclusion: Collectively, homolog clustering via the highly conserved region definition and detection on long non-coding RNAs, as well as the functional explorations on representative sequences in our research, would provide new evidence for the potential function of long non-coding RNAs. Our results on the remarkable roles of long non-coding RNAs would presumably provide a new theoretical basis and candidate diagnostic indicators for tumors.https://www.frontiersin.org/articles/10.3389/fgene.2023.1177259/fullhomolog clusteringHCRXACTLINC00461functional inference |
| spellingShingle | Zhongpeng Liu Tianbin Guo Zhuoda Yin Yanluo Zeng Haiwen Liu Hongyan Yin Functional inference of long non-coding RNAs through exploration of highly conserved regions Frontiers in Genetics homolog clustering HCR XACT LINC00461 functional inference |
| title | Functional inference of long non-coding RNAs through exploration of highly conserved regions |
| title_full | Functional inference of long non-coding RNAs through exploration of highly conserved regions |
| title_fullStr | Functional inference of long non-coding RNAs through exploration of highly conserved regions |
| title_full_unstemmed | Functional inference of long non-coding RNAs through exploration of highly conserved regions |
| title_short | Functional inference of long non-coding RNAs through exploration of highly conserved regions |
| title_sort | functional inference of long non coding rnas through exploration of highly conserved regions |
| topic | homolog clustering HCR XACT LINC00461 functional inference |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1177259/full |
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