Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic Skin
(1) Background: Understanding the function of circular RNAs (circRNAs), a class of noncoding RNA, in psoriatic skin can provide important insights into the complex regulation of genes contributing to the pathogenesis of psoriasis. (2) Methods: A novel method was applied to RNA-seq datasets from 93 s...
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MDPI AG
2021-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/10/5182 |
| _version_ | 1797534185885270016 |
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| author | Xiaoxin Liu Jacqueline Frost Anne Bowcock Weixiong Zhang |
| author_facet | Xiaoxin Liu Jacqueline Frost Anne Bowcock Weixiong Zhang |
| author_sort | Xiaoxin Liu |
| collection | DOAJ |
| description | (1) Background: Understanding the function of circular RNAs (circRNAs), a class of noncoding RNA, in psoriatic skin can provide important insights into the complex regulation of genes contributing to the pathogenesis of psoriasis. (2) Methods: A novel method was applied to RNA-seq datasets from 93 skin biopsy samples to comprehensively identify circRNAs of all types, i.e., canonical circRNAs from the intron-exon junctions of mRNAs and interior circRNAs (i-circRNAs) from the interior regions of exons, introns, and intergenic regions. Selected circRNAs were experimentally validated by qRT-PCR and Sanger sequencing. CircRNAs with abundant and differential expression were identified and their putative function as competing endogenous RNAs (ceRNAs) was analyzed by an integrated analysis of circRNAs, microRNAs, and mRNAs. (3) Results: With a comprehensive search using no information of splicing signals, we systematically identified 179 highly abundant circRNAs in psoriatic skin. Many of these were reported for the first time and many were differentially expressed in involved versus normal or uninvolved skin. Validation based on three additional RNA-seq datasets confirmed most of the identified circRNAs in psoriatic skin. Experimental analyses confirmed the expression of the well-known circRNA CDR1as, a canonical circRNA, and a novel i-circRNA in psoriasis. We also identified many circRNAs that may act as ceRNAs to regulate the expression of mRNA genes in psoriasis-related signaling pathways in psoriasis. (4) Conclusions: The result of the study suggested that circRNAs are abundant in psoriatic skin, have distinct characteristics, and contribute to psoriatic pathogenesis. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T11:26:02Z |
| publishDate | 2021-05-01 |
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| spelling | doaj.art-9a378756a56e4afe8064bc0e7a58ebaa2023-11-21T19:39:43ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-05-012210518210.3390/ijms22105182Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic SkinXiaoxin Liu0Jacqueline Frost1Anne Bowcock2Weixiong Zhang3Institute for Systems Biology, Jianghan University, Wuhan 430056, ChinaDepartment of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USADepartment of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USAInstitute for Systems Biology, Jianghan University, Wuhan 430056, China(1) Background: Understanding the function of circular RNAs (circRNAs), a class of noncoding RNA, in psoriatic skin can provide important insights into the complex regulation of genes contributing to the pathogenesis of psoriasis. (2) Methods: A novel method was applied to RNA-seq datasets from 93 skin biopsy samples to comprehensively identify circRNAs of all types, i.e., canonical circRNAs from the intron-exon junctions of mRNAs and interior circRNAs (i-circRNAs) from the interior regions of exons, introns, and intergenic regions. Selected circRNAs were experimentally validated by qRT-PCR and Sanger sequencing. CircRNAs with abundant and differential expression were identified and their putative function as competing endogenous RNAs (ceRNAs) was analyzed by an integrated analysis of circRNAs, microRNAs, and mRNAs. (3) Results: With a comprehensive search using no information of splicing signals, we systematically identified 179 highly abundant circRNAs in psoriatic skin. Many of these were reported for the first time and many were differentially expressed in involved versus normal or uninvolved skin. Validation based on three additional RNA-seq datasets confirmed most of the identified circRNAs in psoriatic skin. Experimental analyses confirmed the expression of the well-known circRNA CDR1as, a canonical circRNA, and a novel i-circRNA in psoriasis. We also identified many circRNAs that may act as ceRNAs to regulate the expression of mRNA genes in psoriasis-related signaling pathways in psoriasis. (4) Conclusions: The result of the study suggested that circRNAs are abundant in psoriatic skin, have distinct characteristics, and contribute to psoriatic pathogenesis.https://www.mdpi.com/1422-0067/22/10/5182circular RNAcompeting endogenous RNApsoriasisnon-coding RNA |
| spellingShingle | Xiaoxin Liu Jacqueline Frost Anne Bowcock Weixiong Zhang Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic Skin International Journal of Molecular Sciences circular RNA competing endogenous RNA psoriasis non-coding RNA |
| title | Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic Skin |
| title_full | Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic Skin |
| title_fullStr | Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic Skin |
| title_full_unstemmed | Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic Skin |
| title_short | Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic Skin |
| title_sort | canonical and interior circular rnas function as competing endogenous rnas in psoriatic skin |
| topic | circular RNA competing endogenous RNA psoriasis non-coding RNA |
| url | https://www.mdpi.com/1422-0067/22/10/5182 |
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